diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 4ecfbfe33..b290e0901 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -10,15 +10,7 @@
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.
diff --git a/.editorconfig b/.editorconfig
index b6b319077..72dda289a 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -18,7 +18,16 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-indent_size = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore python and markdown
+[*.{py,md}]
+indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 82ce14f40..d784a8bbc 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -9,9 +9,8 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-:::info
-If you need help using or modifying nf-core/rnaseq then the best place to ask is on the nf-core Slack [#rnaseq](https://nfcore.slack.com/channels/rnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
+> [!NOTE]
+> If you need help using or modifying nf-core/rnaseq then the best place to ask is on the nf-core Slack [#rnaseq](https://nfcore.slack.com/channels/rnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
@@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
-receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
 
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
@@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 
diff --git a/.github/include.yaml b/.github/include.yaml
new file mode 100644
index 000000000..a3629f4c4
--- /dev/null
+++ b/.github/include.yaml
@@ -0,0 +1,10 @@
+".":
+  - ./.github/workflows/**
+  - ./nf-test.config
+  - ./nextflow.config
+tests:
+  - ./assets/*
+  - ./bin/*
+  - ./conf/*
+  - ./main.nf
+  - ./nextflow_schema.json
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index d694b7b67..53ecc73d4 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -19,7 +19,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v1
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 66bd47cf9..8346f837c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,288 +1,112 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
-    branches:
-      - dev
   pull_request:
-  release:
-    types: [published]
 
 env:
   NXF_ANSI_LOG: false
+  NFT_VER: "0.9.0"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
-
 jobs:
-  test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}"
+  nf-test-changes:
+    name: Check for changes
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
+    outputs:
+      nf_test_files: ${{ steps.list.outputs.components }}
     steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v4
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+      - uses: actions/checkout@v4
         with:
-          version: "${{ matrix.NXF_VER }}"
+          fetch-depth: 0
 
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.2
         with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          include: .github/include.yaml
 
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
+      - name: print list of nf-test files
         run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
+          echo ${{ steps.list.outputs.components }}
 
-      - name: Run pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
-
-  star_salmon:
-    name: Test STAR Salmon with workflow parameters
-    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
+  test:
+    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    needs: [nf-test-changes]
+    if: needs.nf-test-changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        parameters:
-          - "--skip_qc"
-          - "--skip_trimming"
-          - "--gtf false"
-          - "--star_index false"
-          - "--transcript_fasta false"
-          - "--min_mapped_reads 90"
-          - "--with_umi"
-          - "--with_umi --skip_trimming"
-          - "--remove_ribo_rna --skip_qualimap"
-          - "--bam_csi_index"
-          - "--save_align_intermeds --save_reference"
-          - "--featurecounts_group_type false"
-          - "--trimmer fastp"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
-        with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
-
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with STAR and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+        NXF_VER:
+          - "latest-everything"
+          - "23.04"
+        nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
+        profile:
+          - "docker"
 
-  star_rsem:
-    name: Test STAR RSEM with workflow parameters
-    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc"
-          - "--rsem_index false"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
         with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
+          version: "${{ matrix.NXF_VER }}"
 
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
+          python-version: "3.11"
+          architecture: "x64"
 
-      - name: Replace remote paths in samplesheets
+      - name: Install pdiff to see diff between nf-test snapshots
         run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
+          python -m pip install --upgrade pip
+          pip install pdiff
 
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - uses: nf-core/setup-nf-test@v1
 
-      - name: Run pipeline with RSEM STAR and various parameters
+      - name: Run nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
-  hisat2:
-    name: Test HISAT2 with workflow parameters
-    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc"
-          - "--hisat2_index false"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
+      - uses: pcolby/tap-summary@v1
         with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
+          path: >-
+            test.tap
 
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
-      - name: Install Nextflow
+      - name: Output log on failure
+        if: failure()
         run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
 
-      - name: Run pipeline with HISAT2 and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml
 
-  pseudo:
-    name: Test Pseudoaligners with workflow parameters
-    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
+  confirm-pass:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--pseudo_aligner salmon --skip_qc"
-          - "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment"
-          - "--pseudo_aligner salmon --salmon_index false --transcript_fasta false"
-          - "--pseudo_aligner kallisto --skip_qc"
-          - "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment"
-          - "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false"
+    needs: [test]
+    if: always()
     steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@v3
-        with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
-
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: rnaseq3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with Salmon or Kallisto and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+      - name: All tests ok
+        if: ${{ !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 694e90ecb..0b6b1f272 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v7
+      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
new file mode 100644
index 000000000..2d20d6442
--- /dev/null
+++ b/.github/workflows/download_pipeline.yml
@@ -0,0 +1,86 @@
+name: Test successful pipeline download with 'nf-core download'
+
+# Run the workflow when:
+#  - dispatched manually
+#  - when a PR is opened or reopened to master branch
+#  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
+on:
+  workflow_dispatch:
+    inputs:
+      testbranch:
+        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        required: true
+        default: "dev"
+  pull_request:
+    types:
+      - opened
+      - edited
+      - synchronize
+    branches:
+      - master
+  pull_request_target:
+    branches:
+      - master
+
+env:
+  NXF_ANSI_LOG: false
+
+jobs:
+  download:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.12"
+          architecture: "x64"
+      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install git+https://github.com/nf-core/tools.git@dev
+
+      - name: Get the repository name and current branch set as environment variable
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
+
+      - name: Download the pipeline
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+        run: |
+          nf-core download ${{ env.REPO_LOWERCASE }} \
+          --revision ${{ env.REPO_BRANCH }} \
+          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          --compress "none" \
+          --container-system 'singularity' \
+          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-cache-utilisation 'amend' \
+          --download-configuration
+
+      - name: Inspect download
+        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 619e58a6e..1d7eed3bb 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -4,7 +4,7 @@ on:
     types: [created]
 
 jobs:
-  deploy:
+  fix-linting:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
@@ -13,10 +13,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
@@ -24,32 +31,59 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
+      # Install and run pre-commit
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.12"
 
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "result=pass" >> $GITHUB_OUTPUT
-          else
-            echo "result=fail" >> $GITHUB_OUTPUT
-          fi
+      - name: Run pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
 
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: steps.pre-commit.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: "+1"
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        id: commit-and-push
+        if: steps.pre-commit.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix code linting"
           git push
+
+      - name: react if linting errors were fixed
+        id: react-if-fixed
+        if: steps.commit-and-push.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: hooray
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: confused
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
+            See [CI log](https://github.com/nf-core/rnaseq/actions/runs/${{ github.run_id }}) for more details.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 905c58e44..1fcafe880 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,74 +11,34 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - uses: actions/setup-node@v4
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
-
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  PythonBlack:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+          python-version: "3.12"
 
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -99,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 0bbcd30f2..40acc23f5 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v2
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@v2
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 6ad339277..03ecfcf72 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -9,6 +9,11 @@ jobs:
   toot:
     runs-on: ubuntu-latest
     steps:
+      - name: get topics and convert to hashtags
+        id: get_topics
+        run: |
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
+
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -20,11 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
+
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -56,7 +63,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@v0.0.2
+      - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.gitignore b/.gitignore
index 5124c9ac7..ef809d7c3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,8 +1,12 @@
+*.pyc
+.DS_Store
 .nextflow*
-work/
+.nf-test.log
 data/
+nf-test
+.nf-test*
 results/
-.DS_Store
-testing/
+test.xml
 testing*
-*.pyc
+testing/
+work/
diff --git a/.gitpod.yml b/.gitpod.yml
index acf726953..105a1821a 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -7,15 +7,14 @@ tasks:
   - name: unset JAVA_TOOL_OPTIONS
     command: |
       unset JAVA_TOOL_OPTIONS
+
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - codezombiech.gitignore # Language support for .gitignore files
-    # - cssho.vscode-svgviewer                 # SVG viewer
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    # - nextflow.nextflow                    # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
+    - charliermarsh.ruff # Code linter Ruff
diff --git a/.nf-core.yml b/.nf-core.yml
index 094459361..d01e0a8b4 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,8 +1,15 @@
 repository_type: pipeline
+nf_core_version: "2.14.1"
 lint:
   files_unchanged:
     - assets/email_template.html
     - assets/email_template.txt
-    - lib/NfcoreTemplate.groovy
-    - pyproject.toml
+    - .gitignore
+  files_exist:
+    - conf/modules.config
+  actions_ci: false
   multiqc_config: false
+  modules_config: false
+  nextflow_config:
+    - config_defaults:
+        - params.ribo_database_manifest
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0c31cdb99..4dc0f1dcd 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,13 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e2d4c8fc8..2c3d147f3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,163 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [David Carlson](https://github.com/davidecarlson)
+- [Edmund Miller](https://github.com/edmundmiller)
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Laramie Lindsey](https://github.com/laramiellindsey)
+- [Luke Zappia](https://github.com/lazappi)
+- [Matthias Zepper](https://github.com/MatthiasZepper)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Pieter Moris](https://github.com/pmoris)
+- [Rob Syme](https://github.com/robsyme)
+- [Thomas Danhorn](https://github.com/tdanhorn)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+- [PR #1180](https://github.com/nf-core/rnaseq/pull/1180) - Bump pipeline version to 3.15.0dev
+- [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch)
+- [PR #1197](https://github.com/nf-core/rnaseq/pull/1197) - Delete lib directory and replace with utils\_\* subworkflows
+- [PR #1199](https://github.com/nf-core/rnaseq/pull/1199) - Replace modules.config with more modular config files per module/subworkflow/workflow
+- [PR #1201](https://github.com/nf-core/rnaseq/pull/1201) - Template update for nf-core/tools v2.12
+- [PR #1206](https://github.com/nf-core/rnaseq/pull/1206) - Remove `lib/` directory and `modules.config`
+- [PR #1210](https://github.com/nf-core/rnaseq/pull/1210) - Use pseudoalignment subworkflow components from nf-core/modules
+- [PR #1212](https://github.com/nf-core/rnaseq/pull/1212) - Update all modules and subworkflows to latest versions
+- [PR #1213](https://github.com/nf-core/rnaseq/pull/1213) - Pass transcriptome fasta through to samtools stats
+- [PR #1214](https://github.com/nf-core/rnaseq/pull/1214) - Bump umitools + delocalise prepareforrsem ([#831](https://github.com/nf-core/rnaseq/issues/831))
+- [PR #1216](https://github.com/nf-core/rnaseq/pull/1216) - Delocalise catadditionalfasta ([#1162](https://github.com/nf-core/rnaseq/issues/1162))
+- [PR #1217](https://github.com/nf-core/rnaseq/pull/1217) - Update Emiller88 => edmundmiller in README
+- [PR #1218](https://github.com/nf-core/rnaseq/pull/1218) - Template update for nf-core/tools v2.13
+- [PR #1220](https://github.com/nf-core/rnaseq/pull/1220) - Initialise nf-test and add pipeline level test
+- [PR #1221](https://github.com/nf-core/rnaseq/pull/1221) - Use nf-test test for all nf-core components
+- [PR #1226](https://github.com/nf-core/rnaseq/pull/1226) - Reuse bbsplit index and don't keep overwriting ([#1225](https://github.com/nf-core/rnaseq/issues/1225))
+- [PR #1228](https://github.com/nf-core/rnaseq/pull/1228) - Make README usage consistent with docs/usage.md
+- [PR #1229](https://github.com/nf-core/rnaseq/pull/1229) - Template update for nf-core/tools v2.13.1
+- [PR #1231](https://github.com/nf-core/rnaseq/pull/1231) - Add sortmerna index possibilities
+- [PR #1232](https://github.com/nf-core/rnaseq/pull/1232) - Add nf-test tests to star_genomegenerate_igenomes
+- [PR #1233](https://github.com/nf-core/rnaseq/pull/1233) - Add nf-test tests to star_align_igenomes
+- [PR #1234](https://github.com/nf-core/rnaseq/pull/1234) - Use genomecov from nf-core/modules
+- [PR #1235](https://github.com/nf-core/rnaseq/pull/1235) - Add nf-test tests to utils_nfcore_rnaseq_pipeline tests
+- [PR #1236](https://github.com/nf-core/rnaseq/pull/1236) - Add nf-test tests to gtf_filter
+- [PR #1237](https://github.com/nf-core/rnaseq/pull/1237) - Fix concurrency error in Github CI workflow
+- [PR #1238](https://github.com/nf-core/rnaseq/pull/1238) - Add nf-test tests to preprocess_transcripts_fasta_gencode
+- [PR #1239](https://github.com/nf-core/rnaseq/pull/1239) - Add nf-test tests to align_star
+- [PR #1240](https://github.com/nf-core/rnaseq/pull/1240) - Fix reference files params usage
+- [PR #1241](https://github.com/nf-core/rnaseq/pull/1241) - Add nf-test tests to deseq2_qc
+- [PR #1242](https://github.com/nf-core/rnaseq/pull/1242) - Use dupradar from nf-core/modules
+- [PR #1243](https://github.com/nf-core/rnaseq/pull/1243) - Add nf-test for module MULTIQC_CUSTOM_BIOTYPE
+- [PR #1244](https://github.com/nf-core/rnaseq/pull/1244) - Add gtf2bed tests
+- [PR #1245](https://github.com/nf-core/rnaseq/pull/1245) - nf test quantify rsem
+- [PR #1246](https://github.com/nf-core/rnaseq/pull/1246) - nf-test quantify pseudoalignment
+- [PR #1247](https://github.com/nf-core/rnaseq/pull/1247) - nf-test prepare_genome
+- [PR #1248](https://github.com/nf-core/rnaseq/pull/1248) - Improved ext.args consolidation for STAR and TRIMGALORE extra_args parameters
+- [PR #1249](https://github.com/nf-core/rnaseq/pull/1249) - Include nf-tests for rsem_merge_counts module
+- [PR #1250](https://github.com/nf-core/rnaseq/pull/1250) - Remove all tags.yml files because the testing system has changed
+- [PR #1251](https://github.com/nf-core/rnaseq/pull/1251) - Replace deseq2qc paths
+- [PR #1252](https://github.com/nf-core/rnaseq/pull/1252) - Fix genomeAttribute usage
+- [PR #1253](https://github.com/nf-core/rnaseq/pull/1253) - Use nf-test files as matrix to test over in CI/CD for efficiency
+- [PR #1260](https://github.com/nf-core/rnaseq/pull/1260) - Update CHANGELOG
+- [PR #1261](https://github.com/nf-core/rnaseq/pull/1261) - Add more tests for PREPARE_GENOME
+- [PR #1262](https://github.com/nf-core/rnaseq/pull/1262) - Fix CI pipeline
+- [PR #1264](https://github.com/nf-core/rnaseq/pull/1264) - Add GHA files back into include statement of Github workflow change detection
+- [PR #1265](https://github.com/nf-core/rnaseq/pull/1265) - Small updates noticed during code review
+- [PR #1266](https://github.com/nf-core/rnaseq/pull/1266) - Delete unecessary tags from nf.test files for modules and subworkflows
+- [PR #1271](https://github.com/nf-core/rnaseq/pull/1271) - Update trimming subworkflow to include more tests
+- [PR #1272](https://github.com/nf-core/rnaseq/pull/1272) - Simple pipeline level nf-tests
+- [PR #1274](https://github.com/nf-core/rnaseq/pull/1274) - Update bam_markduplicates_picard subworkflow
+- [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow
+- [PR #1279](https://github.com/nf-core/rnaseq/pull/1279) - Add pseudoaligner pipeline level tests to test suite
+- [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure
+- [PR #1282](https://github.com/nf-core/rnaseq/pull/1282) - Fix CHANGELOG error
+- [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot
+- [PR #1293](https://github.com/nf-core/rnaseq/pull/1293) - Update subworkflow utils_nfcore_pipeline
+- [PR #1297](https://github.com/nf-core/rnaseq/pull/1297) - Important! Template update for nf-core/tools v2.14.1
+- [PR #1302](https://github.com/nf-core/rnaseq/pull/1302) - Add missing files from Tximport processing
+- [PR #1304](https://github.com/nf-core/rnaseq/pull/1304) - Remove redundant gene TPM outputs
+- [PR #1306](https://github.com/nf-core/rnaseq/pull/1306) - Overhaul strandedness detection / comparison
+- [PR #1307](https://github.com/nf-core/rnaseq/pull/1307) - Clarify infer strandedness step in subway map and text
+- [PR #1308](https://github.com/nf-core/rnaseq/pull/1308) - Various MultiQC issues: FastQC sections for raw and trimmed reads // umi-tools dedup and extraction plots, custom content styling.
+- [PR #1309](https://github.com/nf-core/rnaseq/pull/1309) - Document FASTP sampling
+- [PR #1310](https://github.com/nf-core/rnaseq/pull/1310) - Reinstate pseudoalignment subworkflow config
+- [PR #1312](https://github.com/nf-core/rnaseq/pull/1312) - Fix issues with unzipping of GTF/ GFF files without absolute paths
+- [PR #1314](https://github.com/nf-core/rnaseq/pull/1314) - Add reference genome recommendations to usage docs
+- [PR #1317](https://github.com/nf-core/rnaseq/pull/1317) - Strip problematic ifEmpty()
+- [PR #1319](https://github.com/nf-core/rnaseq/pull/1319) - Reinstate oncomplete error messages
+- [PR #1321](https://github.com/nf-core/rnaseq/pull/1321) - Remove push and release triggers from CI
+- [PR #1322](https://github.com/nf-core/rnaseq/pull/1322) - Use pre-built Github Action to detect nf-test changes
+- [PR #1323](https://github.com/nf-core/rnaseq/pull/1323) - Update actions/checkout to v4
+- [PR #1324](https://github.com/nf-core/rnaseq/pull/1324) - Fix tags entries and rename pipeline level tests
+- [PR #1325](https://github.com/nf-core/rnaseq/pull/1325) - Minor fixes to strandedness settings and messaging
+- [PR #1326](https://github.com/nf-core/rnaseq/pull/1326) - Move Conda dependencies for local modules to individual environment file
+- [PR #1328](https://github.com/nf-core/rnaseq/pull/1328) - Add pipeline level test for STAR-RSEM and HISAT2
+- [PR #1329](https://github.com/nf-core/rnaseq/pull/1329) - Remove tags from all nf-test files
+- [PR #1330](https://github.com/nf-core/rnaseq/pull/1330) - Update all nf-core/modules and subworkflows
+- [PR #1331](https://github.com/nf-core/rnaseq/pull/1331) - Adding stubs for local modules
+- [PR #1334](https://github.com/nf-core/rnaseq/pull/1334) - Update all nf-core/modules and subworkflows with stubs
+- [PR #1335](https://github.com/nf-core/rnaseq/pull/1335) - Adding stubs at all levels
+- [PR #1336](https://github.com/nf-core/rnaseq/pull/1336) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD
+- [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance
+- [PR #1341](https://github.com/nf-core/rnaseq/pull/1341) - Add rename in the MultiQC report for samples without techreps
+- [PR #1342](https://github.com/nf-core/rnaseq/pull/1342) - Factor out preprocessing
+- [PR #1345](https://github.com/nf-core/rnaseq/pull/1345) - Fix preprocessing call
+- [PR #1350](https://github.com/nf-core/rnaseq/pull/1350) - Reduce resource usage for sort process in bedtools/genomecov
+- [PR #1352](https://github.com/nf-core/rnaseq/pull/1352) - Assorted fixes to MultiQC usage
+- [PR #1353](https://github.com/nf-core/rnaseq/pull/1353) - Correct conditional for salmon indexing in preprocessing workflow
+- [PR #1355](https://github.com/nf-core/rnaseq/pull/1355) - Make all curves on subway map better looking, and all lines now have the same width
+- [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc
+- [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests
+- [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround
+- [PR #1360](https://github.com/nf-core/rnaseq/pull/1360) - More complete snapshots for pipeline level tests
+- [PR #1361](https://github.com/nf-core/rnaseq/pull/1361) - Animate subway map
+- [PR #1362](https://github.com/nf-core/rnaseq/pull/1362) - Move multiqc module prefix for nf-test to module
+- [PR #1363](https://github.com/nf-core/rnaseq/pull/1363) - Minor updates of nf-core modules and subworkflows
+- [PR #1363](https://github.com/nf-core/rnaseq/pull/1363) - Update dupradar script
+- [PR #1366](https://github.com/nf-core/rnaseq/pull/1366) - Clarify docs on different tximport count files
+- [PR #1367](https://github.com/nf-core/rnaseq/pull/1367) - Clarify design formula and blind dispersion estimation
+- [PR #1370](https://github.com/nf-core/rnaseq/pull/1370) - Bump versions for 3.15.0
+- [PR #1371](https://github.com/nf-core/rnaseq/pull/1371) - Apply Maxime's CHANGELOG edits
+- [PR #1372](https://github.com/nf-core/rnaseq/pull/1372) - Bump tximeta/tximport for gene table row names fix
+
+### Parameters
+
+| Old parameter      | New parameter                    |
+| ------------------ | -------------------------------- |
+|                    | `--pipelines_testdata_base_path` |
+|                    | `--sortmerna_index`              |
+|                    | `--stranded_threshold`           |
+|                    | `--unstranded_threshold`         |
+| `--test_data_base` |                                  |
+
+### Software dependencies
+
+| Dependency                          | Old version | New version |
+| ----------------------------------- | ----------- | ----------- |
+| `bedtools`                          | 2.30.0      | 2.31.1      |
+| `bioconductor-dupradar`             | 1.28.0      | 1.32.0      |
+| `bioconductor-summarizedexperiment` | 1.24.0      | 1.32.0      |
+| `bioconductor-tximeta`              | 1.12.0      | 1.20.1      |
+| `gffread`                           | 0.12.1      | 0.12.7      |
+| `multiqc`                           | 1.20        | 1.22.3      |
+| `picard`                            | 3.0.0       | 3.1.1       |
+| `samtools`                          | 1.17        | 1.20        |
+| `sortmerna`                         | 4.3.4       | 4.3.6       |
+| `umi_tools`                         | 1.14        | 1.15        |
+| `untar`                             | 1.3         | 1.34        |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[3.14.0](https://github.com/nf-core/rnaseq/releases/tag/3.14.0)] - 2024-01-08
 
 ### Credits
diff --git a/README.md b/README.md
index 9e3b4641a..c5f58478e 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,18 @@
-# ![nf-core/rnaseq](docs/images/nf-core-rnaseq_logo_light.png#gh-light-mode-only) ![nf-core/rnaseq](docs/images/nf-core-rnaseq_logo_dark.png#gh-dark-mode-only)
+<h1>
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-rnaseq_logo_dark.png">
+    <img alt="nf-core/rnaseq" src="docs/images/nf-core-rnaseq_logo_light.png">
+  </picture>
+</h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)
+[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnaseq)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnaseq)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
@@ -15,10 +20,12 @@
 
 **nf-core/rnaseq** is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report.
 
-![nf-core/rnaseq metro map](docs/images/nf-core-rnaseq_metro_map_grey.png)
+![nf-core/rnaseq metro map](docs/images/nf-core-rnaseq_metro_map_grey_animated.svg)
+
+> In case the image above is not loading, please have a look at the [static version](docs/images/nf-core-rnaseq_metro_map_grey.png).
 
 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))
-2. Sub-sample FastQ files and auto-infer strandedness ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/))
+2. Auto-infer strandedness by subsampling and pseudoalignment ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/))
 3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 4. UMI extraction ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))
 5. Adapter and quality trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))
@@ -75,9 +82,10 @@ Now, you can run the pipeline using:
 
 ```bash
 nextflow run nf-core/rnaseq \
-    --input samplesheet.csv \
+    --input <SAMPLESHEET> \
     --outdir <OUTDIR> \
-    --genome GRCh37 \
+    --gtf <GTF> \
+    --fasta <GENOME FASTA> \
     -profile <docker/singularity/.../institute>
 ```
 
@@ -114,7 +122,7 @@ Many thanks to other who have helped out along the way too, including (but not l
 - [Alex Peltzer](https://github.com/apeltzer)
 - [Colin Davenport](https://github.com/colindaven)
 - [Denis Moreno](https://github.com/Galithil)
-- [Edmund Miller](https://github.com/Emiller88)
+- [Edmund Miller](https://github.com/edmundmiller)
 - [Gregor Sturm](https://github.com/grst)
 - [Jacki Buros Novik](https://github.com/jburos)
 - [Lorena Pantano](https://github.com/lpantano)
diff --git a/assets/dummy_file.txt b/assets/dummy_file.txt
deleted file mode 100644
index 8b1378917..000000000
--- a/assets/dummy_file.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/assets/email_template.html b/assets/email_template.html
index 0ef39b222..dc46d39ee 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -14,7 +14,7 @@
     <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto">
       <img src="cid:nfcorepipelinelogo" />
 
-      <h1>nf-core/rnaseq v${version}</h1>
+      <h1>nf-core/rnaseq ${version}</h1>
       <h2>Run Name: $runName</h2>
 
       <% if (!success){ out << """
diff --git a/assets/email_template.txt b/assets/email_template.txt
index 5440f887a..8789fd8ae 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -4,7 +4,7 @@
   |\\ | |__  __ /  ` /  \\ |__) |__         }  {
   | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
                                         `._,._,'
-  nf-core/rnaseq v${version}
+  nf-core/rnaseq ${version}
 ----------------------------------------------------
 Run Name: $runName
 
diff --git a/assets/nf-core-rnaseq_logo_light.png b/assets/nf-core-rnaseq_logo_light.png
index b0c99cb83..87c1d5f1d 100644
Binary files a/assets/nf-core-rnaseq_logo_light.png and b/assets/nf-core-rnaseq_logo_light.png differ
diff --git a/bin/deseq2_qc.r b/bin/deseq2_qc.r
index 14bd48f70..d55180400 100755
--- a/bin/deseq2_qc.r
+++ b/bin/deseq2_qc.r
@@ -92,7 +92,8 @@ if (decompose) {
 DDSFile <- paste(opt$outprefix,".dds.RData",sep="")
 
 counts  <- count.table[,samples.vec,drop=FALSE]
-dds     <- DESeqDataSetFromMatrix(countData=round(counts), colData=coldata, design=~ 1)
+# `design=~1` creates intercept-only model, equivalent to setting `blind=TRUE` for transformation.
+dds     <- DESeqDataSetFromMatrix(countData=round(counts), colData=coldata, design=~1)
 dds     <- estimateSizeFactors(dds)
 if (min(dim(count.table))<=1)  { # No point if only one sample, or one gene
     save(dds,file=DDSFile)
diff --git a/bin/dupradar.r b/bin/dupradar.r
deleted file mode 100755
index 00119f550..000000000
--- a/bin/dupradar.r
+++ /dev/null
@@ -1,153 +0,0 @@
-#!/usr/bin/env Rscript
-
-# Written by Phil Ewels and released under the MIT license.
-
-# Command line argument processing
-args = commandArgs(trailingOnly=TRUE)
-if (length(args) < 5) {
-    stop("Usage: dupRadar.r <input.bam> <annotation.gtf> <strandDirection:0=unstranded/1=forward/2=reverse> <paired/single> <nbThreads> <R-package-location (optional)>", call.=FALSE)
-}
-input_bam <- args[1]
-output_prefix <- args[2]
-annotation_gtf <- args[3]
-stranded <- as.numeric(args[4])
-paired_end <- if(args[5]=='paired') TRUE else FALSE
-threads <- as.numeric(args[6])
-
-bamRegex <- "(.+)\\.bam$"
-
-if(!(grepl(bamRegex, input_bam) && file.exists(input_bam) &&  (!file.info(input_bam)$isdir))) stop("First argument '<input.bam>' must be an existing file (not a directory) with '.bam' extension...")
-if(!(file.exists(annotation_gtf) &&  (!file.info(annotation_gtf)$isdir))) stop("Second argument '<annotation.gtf>' must be an existing file (and not a directory)...")
-if(is.na(stranded) || (!(stranded %in% (0:2)))) stop("Third argument <strandDirection> must be a numeric value in 0(unstranded)/1(forward)/2(reverse)...")
-if(is.na(threads) || (threads<=0)) stop("Fifth argument <nbThreads> must be a strictly positive numeric value...")
-
-# Debug messages (stderr)
-message("Input bam      (Arg 1): ", input_bam)
-message("Input gtf      (Arg 2): ", annotation_gtf)
-message("Strandness     (Arg 3): ", c("unstranded", "forward", "reverse")[stranded+1])
-message("paired/single  (Arg 4): ", ifelse(paired_end, 'paired', 'single'))
-message("Nb threads     (Arg 5): ", threads)
-message("R package loc. (Arg 6): ", ifelse(length(args) > 4, args[5], "Not specified"))
-message("Output basename       : ", output_prefix)
-
-
-# Load / install packages
-if (length(args) > 5) { .libPaths( c( args[6], .libPaths() ) ) }
-if (!require("dupRadar")){
-    source("http://bioconductor.org/biocLite.R")
-    biocLite("dupRadar", suppressUpdates=TRUE)
-    library("dupRadar")
-}
-if (!require("parallel")) {
-    install.packages("parallel", dependencies=TRUE, repos='http://cloud.r-project.org/')
-    library("parallel")
-}
-
-# Duplicate stats
-dm <- analyzeDuprates(input_bam, annotation_gtf, stranded, paired_end, threads)
-write.table(dm, file=paste(output_prefix, "_dupMatrix.txt", sep=""), quote=F, row.name=F, sep="\t")
-
-# 2D density scatter plot
-pdf(paste0(output_prefix, "_duprateExpDens.pdf"))
-duprateExpDensPlot(DupMat=dm)
-title("Density scatter plot")
-mtext(output_prefix, side=3)
-dev.off()
-fit <- duprateExpFit(DupMat=dm)
-cat(
-    paste("- dupRadar Int (duprate at low read counts):", fit$intercept),
-    paste("- dupRadar Sl (progression of the duplication rate):", fit$slope),
-    fill=TRUE, labels=output_prefix,
-    file=paste0(output_prefix, "_intercept_slope.txt"), append=FALSE
-)
-
-# Create a multiqc file dupInt
-sample_name <- gsub("Aligned.sortedByCoord.out.markDups", "", output_prefix)
-line="#id: DupInt
-#plot_type: 'generalstats'
-#pconfig:
-#    dupRadar_intercept:
-#        title: 'dupInt'
-#        namespace: 'DupRadar'
-#        description: 'Intercept value from DupRadar'
-#        max: 100
-#        min: 0
-#        scale: 'RdYlGn-rev'
-#        format: '{:.2f}%'
-Sample dupRadar_intercept"
-
-write(line,file=paste0(output_prefix, "_dup_intercept_mqc.txt"),append=TRUE)
-write(paste(sample_name, fit$intercept),file=paste0(output_prefix, "_dup_intercept_mqc.txt"),append=TRUE)
-
-# Get numbers from dupRadar GLM
-curve_x <- sort(log10(dm$RPK))
-curve_y = 100*predict(fit$glm, data.frame(x=curve_x), type="response")
-# Remove all of the infinite values
-infs = which(curve_x %in% c(-Inf,Inf))
-curve_x = curve_x[-infs]
-curve_y = curve_y[-infs]
-# Reduce number of data points
-curve_x <- curve_x[seq(1, length(curve_x), 10)]
-curve_y <- curve_y[seq(1, length(curve_y), 10)]
-# Convert x values back to real counts
-curve_x = 10^curve_x
-# Write to file
-line="#id: dupradar
-#plot_type: 'linegraph'
-#section_name: 'DupRadar'
-#section_href: 'bioconductor.org/packages/release/bioc/html/dupRadar.html'
-#description: \"provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication.
-#    This plot shows the general linear models - a summary of the gene duplication distributions. \"
-#pconfig:
-#    title: 'DupRadar General Linear Model'
-#    xLog: True
-#    xlab: 'expression (reads/kbp)'
-#    ylab: '% duplicate reads'
-#    ymax: 100
-#    ymin: 0
-#    tt_label: '<b>{point.x:.1f} reads/kbp</b>: {point.y:,.2f}% duplicates'
-#    xPlotLines:
-#        - color: 'green'
-#          dashStyle: 'LongDash'
-#          label:
-#                style: {color: 'green'}
-#                text: '0.5 RPKM'
-#                verticalAlign: 'bottom'
-#                y: -65
-#          value: 0.5
-#          width: 1
-#        - color: 'red'
-#          dashStyle: 'LongDash'
-#          label:
-#                style: {color: 'red'}
-#                text: '1 read/bp'
-#                verticalAlign: 'bottom'
-#                y: -65
-#          value: 1000
-#          width: 1"
-
-write(line,file=paste0(output_prefix, "_duprateExpDensCurve_mqc.txt"),append=TRUE)
-write.table(
-    cbind(curve_x, curve_y),
-    file=paste0(output_prefix, "_duprateExpDensCurve_mqc.txt"),
-    quote=FALSE, row.names=FALSE, col.names=FALSE, append=TRUE,
-)
-
-# Distribution of expression box plot
-pdf(paste0(output_prefix, "_duprateExpBoxplot.pdf"))
-duprateExpBoxplot(DupMat=dm)
-title("Percent Duplication by Expression")
-mtext(output_prefix, side=3)
-dev.off()
-
-# Distribution of RPK values per gene
-pdf(paste0(output_prefix, "_expressionHist.pdf"))
-expressionHist(DupMat=dm)
-title("Distribution of RPK values per gene")
-mtext(output_prefix, side=3)
-dev.off()
-
-# Print sessioninfo to standard out
-print(output_prefix)
-citation("dupRadar")
-sessionInfo()
diff --git a/bin/fasta2gtf.py b/bin/fasta2gtf.py
deleted file mode 100755
index 716ee06ce..000000000
--- a/bin/fasta2gtf.py
+++ /dev/null
@@ -1,88 +0,0 @@
-#!/usr/bin/env python3
-
-# Written by Pranathi Vemuri and released under the MIT license.
-
-"""
-Read a custom fasta file and create a custom GTF containing each entry
-"""
-import argparse
-from itertools import groupby
-import logging
-
-# Create a logger
-logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
-logger = logging.getLogger(__file__)
-logger.setLevel(logging.INFO)
-
-
-def fasta_iter(fasta_name):
-    """
-    modified from Brent Pedersen
-    Correct Way To Parse A Fasta File In Python
-    given a fasta file. yield tuples of header, sequence
-
-    Fasta iterator from https://www.biostars.org/p/710/#120760
-    """
-    with open(fasta_name) as fh:
-        # ditch the boolean (x[0]) and just keep the header or sequence since
-        # we know they alternate.
-        faiter = (x[1] for x in groupby(fh, lambda line: line[0] == ">"))
-        for header in faiter:
-            # drop the ">"
-            headerStr = header.__next__()[1:].strip()
-
-            # join all sequence lines to one.
-            seq = "".join(s.strip() for s in faiter.__next__())
-
-            yield (headerStr, seq)
-
-
-def fasta2gtf(fasta, output, biotype):
-    fiter = fasta_iter(fasta)
-    # GTF output lines
-    lines = []
-    attributes = 'exon_id "{name}.1"; exon_number "1";{biotype} gene_id "{name}_gene"; gene_name "{name}_gene"; gene_source "custom"; transcript_id "{name}_gene"; transcript_name "{name}_gene";\n'
-    line_template = "{name}\ttransgene\texon\t1\t{length}\t.\t+\t.\t" + attributes
-
-    for ff in fiter:
-        name, seq = ff
-        # Use first ID as separated by spaces as the "sequence name"
-        # (equivalent to "chromosome" in other cases)
-        seqname = name.split()[0]
-        # Remove all spaces
-        name = seqname.replace(" ", "_")
-        length = len(seq)
-        biotype_attr = ""
-        if biotype:
-            biotype_attr = f' {biotype} "transgene";'
-        line = line_template.format(name=name, length=length, biotype=biotype_attr)
-        lines.append(line)
-
-    with open(output, "w") as f:
-        f.write("".join(lines))
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description="""Convert a custom fasta (e.g. transgene)
-        to a GTF annotation."""
-    )
-    parser.add_argument("fasta", type=str, help="Custom transgene sequence")
-    parser.add_argument(
-        "-o",
-        "--output",
-        dest="output",
-        default="transgenes.gtf",
-        type=str,
-        help="Gene annotation GTF output",
-    )
-    parser.add_argument(
-        "-b",
-        "--biotype",
-        dest="biotype",
-        default="",
-        type=str,
-        help="Name of gene biotype attribute to use in last column of GTF entry",
-    )
-    args = parser.parse_args()
-    fasta2gtf(args.fasta, args.output, args.biotype)
diff --git a/bin/mqc_features_stat.py b/bin/mqc_features_stat.py
index fa69b231c..b0577cd5f 100755
--- a/bin/mqc_features_stat.py
+++ b/bin/mqc_features_stat.py
@@ -21,8 +21,7 @@
 #        description: '% reads overlapping {ft} features'
 #        max: 100
 #        min: 0
-#        scale: 'RdYlGn-rev'
-#        format: '{{:.2f}}%'"""
+#        scale: 'RdYlGn-rev'"""
 
 
 def mqc_feature_stat(bfile, features, outfile, sname=None):
diff --git a/bin/prepare-for-rsem.py b/bin/prepare-for-rsem.py
deleted file mode 100755
index f874af792..000000000
--- a/bin/prepare-for-rsem.py
+++ /dev/null
@@ -1,270 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Credits
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This script is a clone of the "prepare-for-rsem.py" script written by
-Ian Sudbury, Tom Smith and other contributors to the UMI-tools package:
-https://github.com/CGATOxford/UMI-tools
-
-It has been included here to address problems encountered with
-Salmon quant and RSEM as discussed in the issue below:
-https://github.com/CGATOxford/UMI-tools/issues/465
-
-When the "umi_tools prepare-for-rsem" command becomes available in an official
-UMI-tools release this script will be replaced and deprecated.
-
-Commit:
-https://github.com/CGATOxford/UMI-tools/blob/bf8608d6a172c5ca0dcf33c126b4e23429177a72/umi_tools/prepare-for-rsem.py
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-prepare_for_rsem - make the output from dedup or group compatible with RSEM
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-The SAM format specification states that the mnext and mpos fields should point
-to the primary alignment of a read's mate. However, not all aligners adhere to
-this standard. In addition, the RSEM software requires that the mate of a read1
-appears directly after it in its input BAM. This requires that there is exactly
-one read1 alignment for every read2 and vice versa.
-
-In general (except in a few edge cases) UMI tools outputs only the read2 to that
-corresponds to the read specified in the mnext and mpos positions of a selected
-read1, and only outputs this read once, even if multiple read1s point to it.
-This makes UMI-tools outputs incompatible with RSEM. This script takes the output
-from dedup or groups and ensures that each read1 has exactly one read2 (and vice
-versa), that read2 always appears directly after read1,and that pairs point to
-each other (note this is technically not valid SAM format). Copy any specified
-tags from read1 to read2 if they are present (by default, UG and BX, the unique
-group and correct UMI tags added by _group_)
-
-Input must to name sorted.
-
-
-https://raw.githubusercontent.com/CGATOxford/UMI-tools/master/LICENSE
-
-"""
-
-from umi_tools import Utilities as U
-from collections import defaultdict, Counter
-import pysam
-import sys
-
-usage = """
-prepare_for_rsem - make output from dedup or group compatible with RSEM
-
-Usage: umi_tools prepare_for_rsem [OPTIONS] [--stdin=IN_BAM] [--stdout=OUT_BAM]
-
-       note: If --stdout is omited, standard out is output. To
-             generate a valid BAM file on standard out, please
-             redirect log with --log=LOGFILE or --log2stderr """
-
-
-def chunk_bam(bamfile):
-    """Take in a iterator of pysam.AlignmentSegment entries and yield
-    lists of reads that all share the same name"""
-
-    last_query_name = None
-    output_buffer = list()
-
-    for read in bamfile:
-        if last_query_name is not None and last_query_name != read.query_name:
-            yield (output_buffer)
-            output_buffer = list()
-
-        last_query_name = read.query_name
-        output_buffer.append(read)
-
-    yield (output_buffer)
-
-
-def copy_tags(tags, read1, read2):
-    """Given a  list of tags, copies the values of these tags from read1
-    to read2, if the tag is set"""
-
-    for tag in tags:
-        try:
-            read1_tag = read1.get_tag(tag, with_value_type=True)
-            read2.set_tag(tag, value=read1_tag[0], value_type=read1_tag[1])
-        except KeyError:
-            pass
-
-    return read2
-
-
-def pick_mate(read, template_dict, mate_key):
-    """Find the mate of read in the template dict using key. It will retrieve
-    all reads at that key, and then scan to pick the one that refers to _read_
-    as it's mate. If there is no such read, it picks a first one it comes to"""
-
-    mate = None
-
-    # get a list of secondary reads at the correct alignment position
-    potential_mates = template_dict[not read.is_read1][mate_key]
-
-    # search through one at a time to find a read that points to the current read
-    # as its mate.
-    for candidate_mate in potential_mates:
-        if (
-            candidate_mate.next_reference_name == read.reference_name
-            and candidate_mate.next_reference_start == read.pos
-        ):
-            mate = candidate_mate
-
-    # if no such read is found, then pick any old secondary alignment at that position
-    # note: this happens when UMI-tools outputs the wrong read as something's pair.
-    if mate is None and len(potential_mates) > 0:
-        mate = potential_mates[0]
-
-    return mate
-
-
-def main(argv=None):
-    if argv is None:
-        argv = sys.argv
-
-    # setup command line parser
-    parser = U.OptionParser(version="%prog version: $Id$", usage=usage, description=globals()["__doc__"])
-    group = U.OptionGroup(parser, "RSEM preparation specific options")
-
-    group.add_option(
-        "--tags",
-        dest="tags",
-        type="string",
-        default="UG,BX",
-        help="Comma-separated list of tags to transfer from read1 to read2",
-    )
-    group.add_option(
-        "--sam", dest="sam", action="store_true", default=False, help="input and output SAM rather than BAM"
-    )
-
-    parser.add_option_group(group)
-
-    # add common options (-h/--help, ...) and parse command line
-    (options, args) = U.Start(
-        parser, argv=argv, add_group_dedup_options=False, add_umi_grouping_options=False, add_sam_options=False
-    )
-
-    skipped_stats = Counter()
-
-    if options.stdin != sys.stdin:
-        in_name = options.stdin.name
-        options.stdin.close()
-    else:
-        in_name = "-"
-
-    if options.sam:
-        mode = ""
-    else:
-        mode = "b"
-
-    inbam = pysam.AlignmentFile(in_name, "r" + mode)
-
-    if options.stdout != sys.stdout:
-        out_name = options.stdout.name
-        options.stdout.close()
-    else:
-        out_name = "-"
-
-    outbam = pysam.AlignmentFile(out_name, "w" + mode, template=inbam)
-
-    options.tags = options.tags.split(",")
-
-    for template in chunk_bam(inbam):
-        assert len(set(r.query_name for r in template)) == 1
-        current_template = {True: defaultdict(list), False: defaultdict(list)}
-
-        for read in template:
-            key = (read.reference_name, read.pos, not read.is_secondary)
-            current_template[read.is_read1][key].append(read)
-
-        output = set()
-
-        for read in template:
-            mate = None
-
-            # if this read is a non_primary alignment, we first want to check if it has a mate
-            # with the non-primary alignment flag set.
-
-            mate_key_primary = True
-            mate_key_secondary = (read.next_reference_name, read.next_reference_start, False)
-
-            # First look for a read that has the same primary/secondary status
-            # as read (i.e. secondary mate for secondary read, and primary mate
-            # for primary read)
-            mate_key = (read.next_reference_name, read.next_reference_start, read.is_secondary)
-            mate = pick_mate(read, current_template, mate_key)
-
-            # If none was found then look for the opposite (primary mate of secondary
-            # read or seconadary mate of primary read)
-            if mate is None:
-                mate_key = (read.next_reference_name, read.next_reference_start, not read.is_secondary)
-                mate = pick_mate(read, current_template, mate_key)
-
-            # If we still don't have a mate, then their can't be one?
-            if mate is None:
-                skipped_stats["no_mate"] += 1
-                U.warn(
-                    "Alignment {} has no mate -- skipped".format(
-                        "\t".join(map(str, [read.query_name, read.flag, read.reference_name, int(read.pos)]))
-                    )
-                )
-                continue
-
-            # because we might want to make changes to the read, but not have those changes reflected
-            # if we need the read again,we copy the read. This is only way I can find to do this.
-            read = pysam.AlignedSegment().from_dict(read.to_dict(), read.header)
-            mate = pysam.AlignedSegment().from_dict(mate.to_dict(), read.header)
-
-            # Make it so that if our read is secondary, the mate is also secondary. We don't make the
-            # mate primary if the read is primary because we would otherwise end up with mulitple
-            # primary alignments.
-            if read.is_secondary:
-                mate.is_secondary = True
-
-            # In a situation where there is already one mate for each read, then we will come across
-            # each pair twice - once when we scan read1 and once when we scan read2. Thus we need
-            # to make sure we don't output something already output.
-            if read.is_read1:
-                mate = copy_tags(options.tags, read, mate)
-                output_key = str(read) + str(mate)
-
-                if output_key not in output:
-                    output.add(output_key)
-                    outbam.write(read)
-                    outbam.write(mate)
-                    skipped_stats["pairs_output"] += 1
-
-            elif read.is_read2:
-                read = copy_tags(options.tags, mate, read)
-                output_key = str(mate) + str(read)
-
-                if output_key not in output:
-                    output.add(output_key)
-                    outbam.write(mate)
-                    outbam.write(read)
-                    skipped_stats["pairs_output"] += 1
-
-            else:
-                skipped_stats["skipped_not_read12"] += 1
-                U.warn(
-                    "Alignment {} is neither read1 nor read2 -- skipped".format(
-                        "\t".join(map(str, [read.query_name, read.flag, read.reference_name, int(read.pos)]))
-                    )
-                )
-                continue
-
-    if not out_name == "-":
-        outbam.close()
-
-    U.info(
-        "Total pairs output: {}, Pairs skipped - no mates: {},"
-        " Pairs skipped - not read1 or 2: {}".format(
-            skipped_stats["pairs_output"], skipped_stats["no_mate"], skipped_stats["skipped_not_read12"]
-        )
-    )
-    U.Stop()
-
-
-if __name__ == "__main__":
-    sys.exit(main(sys.argv))
diff --git a/bin/summarizedexperiment.r b/bin/summarizedexperiment.r
deleted file mode 100755
index 767d542c7..000000000
--- a/bin/summarizedexperiment.r
+++ /dev/null
@@ -1,70 +0,0 @@
-#!/usr/bin/env Rscript
-
-# Written by Lorena Pantano and released under the MIT license.
-
-library(SummarizedExperiment)
-
-## Create SummarizedExperiment (se) object from counts
-
-args <- commandArgs(trailingOnly = TRUE)
-if (length(args) < 3) {
-    stop("Usage: summarizedexperiment.r <coldata> <counts> <tpm> <tx2gene>", call. = FALSE)
-}
-
-coldata <- args[1]
-counts_fn <- args[2]
-tpm_fn <- args[3]
-tx2gene <- args[4]
-
-info <- file.info(tx2gene)
-if (info$size == 0) {
-    tx2gene <- NULL
-} else {
-    rowdata <- read.csv(tx2gene, sep = "\t", header = FALSE)
-    colnames(rowdata) <- c("tx", "gene_id", "gene_name")
-    tx2gene <- rowdata[, 1:2]
-}
-
-counts <- read.csv(counts_fn, row.names = 1, sep = "\t")
-counts <- counts[, 2:ncol(counts), drop = FALSE] # remove gene_name column
-tpm <- read.csv(tpm_fn, row.names = 1, sep = "\t")
-tpm <- tpm[, 2:ncol(tpm), drop = FALSE] # remove gene_name column
-
-if (length(intersect(rownames(counts), rowdata[["tx"]])) > length(intersect(rownames(counts), rowdata[["gene_id"]]))) {
-    by_what <- "tx"
-} else {
-    by_what <- "gene_id"
-    rowdata <- unique(rowdata[, 2:3])
-}
-
-if (file.exists(coldata)) {
-    coldata <- read.csv(coldata, sep = "\t")
-    coldata <- coldata[match(colnames(counts), coldata[, 1]), ]
-    coldata <- cbind(files = fns, coldata)
-} else {
-    message("ColData not avaliable ", coldata)
-    coldata <- data.frame(files = colnames(counts), names = colnames(counts))
-}
-
-rownames(coldata) <- coldata[["names"]]
-extra <- setdiff(rownames(counts), as.character(rowdata[[by_what]]))
-if (length(extra) > 0) {
-    rowdata <- rbind(
-        rowdata,
-        data.frame(
-            tx = extra,
-            gene_id = extra,
-            gene_name = extra
-        )[, colnames(rowdata)]
-    )
-}
-
-rowdata <- rowdata[match(rownames(counts), as.character(rowdata[[by_what]])), ]
-rownames(rowdata) <- rowdata[[by_what]]
-se <- SummarizedExperiment(
-    assays = list(counts = counts, abundance = tpm),
-    colData = DataFrame(coldata),
-    rowData = rowdata
-)
-
-saveRDS(se, file = paste0(tools::file_path_sans_ext(counts_fn), ".rds"))
diff --git a/bin/tximport.r b/bin/tximport.r
deleted file mode 100755
index 59a8fcd9e..000000000
--- a/bin/tximport.r
+++ /dev/null
@@ -1,143 +0,0 @@
-#!/usr/bin/env Rscript
-
-# Script for importing and processing transcript-level quantifications.
-# Written by Lorena Pantano, later modified by Jonathan Manning, and released
-# under the MIT license.
-
-# Loading required libraries
-library(SummarizedExperiment)
-library(tximport)
-
-# Parsing command line arguments
-args <- commandArgs(trailingOnly=TRUE)
-if (length(args) < 4) {
-    stop("Usage: tximport.r <coldata_path> <path> <prefix> <quant_type> <tx2gene_path>",
-        call.=FALSE)
-}
-
-# Assigning command line arguments to variables
-coldata_path <- args[1]
-path <- args[2]
-prefix <- args[3]
-quant_type <- args[4]
-tx2gene_path <- args[5]
-
-## Functions
-
-# Build a table from a SummarizedExperiment object
-build_table <- function(se.obj, slot) {
-    cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]])
-}
-
-# Write a table to a file with given parameters
-write_se_table <- function(params) {
-    file_name <- paste0(prefix, ".", params$suffix)
-    write.table(build_table(params$obj, params$slot), file_name,
-                sep="\t", quote=FALSE, row.names = FALSE)
-}
-
-# Read transcript metadata from a given path
-read_transcript_info <- function(tinfo_path){
-    info <- file.info(tinfo_path)
-    if (info$size == 0) {
-        stop("tx2gene file is empty")
-    }
-
-    transcript_info <- read.csv(tinfo_path, sep="\t", header = FALSE,
-                                col.names = c("tx", "gene_id", "gene_name"))
-
-    extra <- setdiff(rownames(txi[[1]]), as.character(transcript_info[["tx"]]))
-    transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra))
-    transcript_info <- transcript_info[match(rownames(txi[[1]]), transcript_info[["tx"]]), ]
-    rownames(transcript_info) <- transcript_info[["tx"]]
-
-    list(transcript = transcript_info,
-        gene = unique(transcript_info[,2:3]),
-        tx2gene = transcript_info[,1:2])
-}
-
-# Read and process sample/column data from a given path
-read_coldata <- function(coldata_path){
-    if (file.exists(coldata_path)) {
-        coldata <- read.csv(coldata_path, sep="\t")
-        coldata <- coldata[match(names, coldata[,1]),]
-        coldata <- cbind(files = fns, coldata)
-    } else {
-        message("ColData not available: ", coldata_path)
-        coldata <- data.frame(files = fns, names = names)
-    }
-    rownames(coldata) <- coldata[["names"]]
-}
-
-# Create a SummarizedExperiment object with given data
-create_summarized_experiment <- function(counts, abundance, length, col_data, row_data) {
-    SummarizedExperiment(assays = list(counts = counts, abundance = abundance, length = length),
-        colData = col_data,
-        rowData = row_data)
-}
-
-# Main script starts here
-
-# Define pattern for file names based on quantification type
-pattern <- ifelse(quant_type == "kallisto", "abundance.tsv", "quant.sf")
-fns <- list.files(path, pattern = pattern, recursive = T, full.names = T)
-names <- basename(dirname(fns))
-names(fns) <- names
-dropInfReps <- quant_type == "kallisto"
-
-# Import transcript-level quantifications
-txi <- tximport(fns, type = quant_type, txOut = TRUE, dropInfReps = dropInfReps)
-
-# Read transcript and sample data
-transcript_info <- read_transcript_info(tx2gene_path)
-coldata <- read_coldata(coldata_path)
-
-# Create initial SummarizedExperiment object
-se <- create_summarized_experiment(txi[["counts"]], txi[["abundance"]], txi[["length"]],
-    DataFrame(coldata), transcript_info$transcript)
-
-# Setting parameters for writing tables
-params <- list(
-    list(obj = se, slot = "abundance", suffix = "transcript_tpm.tsv"),
-    list(obj = se, slot = "counts", suffix = "transcript_counts.tsv"),
-    list(obj = se, slot = "length", suffix = "transcript_lengths.tsv")
-)
-
-# Process gene-level data if tx2gene mapping is available
-if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info$tx2gene)) {
-    tx2gene <- transcript_info$tx2gene
-    gi <- summarizeToGene(txi, tx2gene = tx2gene)
-    gi.ls <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM")
-    gi.s <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "scaledTPM")
-
-    gene_info <- transcript_info$gene[match(rownames(gi[[1]]), transcript_info$gene[["gene_id"]]),]
-    rownames(gene_info) <- gene_info[["tx"]]
-
-    col_data_frame <- DataFrame(coldata)
-
-    # Create gene-level SummarizedExperiment objects
-    gse <- create_summarized_experiment(gi[["counts"]], gi[["abundance"]], gi[["length"]],
-        col_data_frame, gene_info)
-    gse.ls <- create_summarized_experiment(gi.ls[["counts"]], gi.ls[["abundance"]], gi.ls[["length"]],
-        col_data_frame, gene_info)
-    gse.s <- create_summarized_experiment(gi.s[["counts"]], gi.s[["abundance"]], gi.s[["length"]],
-        col_data_frame, gene_info)
-
-    params <- c(params, list(
-        list(obj = gse, slot = "length", suffix = "gene_lengths.tsv"),
-        list(obj = gse, slot = "abundance", suffix = "gene_tpm.tsv"),
-        list(obj = gse, slot = "counts", suffix = "gene_counts.tsv"),
-        list(obj = gse.ls, slot = "abundance", suffix = "gene_tpm_length_scaled.tsv"),
-        list(obj = gse.ls, slot = "counts", suffix = "gene_counts_length_scaled.tsv"),
-        list(obj = gse.s, slot = "abundance", suffix = "gene_tpm_scaled.tsv"),
-        list(obj = gse.s, slot = "counts", suffix = "gene_counts_scaled.tsv")
-    ))
-}
-
-# Writing tables for each set of parameters
-done <- lapply(params, write_se_table)
-
-# Output session information and citations
-citation("tximeta")
-sessionInfo()
-
diff --git a/conf/base.config b/conf/base.config
index 337564e5c..93ad25b28 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -57,7 +57,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
deleted file mode 100644
index 16d635cdb..000000000
--- a/conf/modules.config
+++ /dev/null
@@ -1,1167 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
-----------------------------------------------------------------------------------------
-*/
-
-def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
-
-//
-// General configuration options
-//
-
-process {
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
-    withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-}
-
-//
-// Genome preparation options
-//
-
-process {
-    withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'UNTAR_.*' {
-        ext.args2 = '--no-same-owner'
-    }
-
-    withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'GFFREAD' {
-        ext.args   = '--keep-exon-attrs -F -T'
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'HISAT2_EXTRACTSPLICESITES' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'SALMON_INDEX' {
-        ext.args   = { [
-                params.gencode ? '--gencode' : '',
-                params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}": ''
-        ].join(' ').trim() }
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'KALLISTO_INDEX' {
-        ext.args   = params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}" : ''
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'RSEM_PREPAREREFERENCE_GENOME' {
-        ext.args   = '--star'
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'GTF2BED' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'GTF_FILTER' {
-        ext.args   = { params.skip_gtf_transcript_filter ?: '--skip_transcript_id_check' }
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'CUSTOM_GETCHROMSIZES' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'CAT_FASTQ' {
-        publishDir = [
-            path: { params.save_merged_fastq ? "${params.outdir}/fastq" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename.endsWith('.fastq.gz') && params.save_merged_fastq) ? filename : null }
-        ]
-    }
-}
-
-if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
-    process {
-        withName: '.*:PREPARE_GENOME:BBMAP_BBSPLIT' {
-            ext.args   = 'build=1'
-            publishDir = [
-                path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-            ]
-        }
-    }
-}
-
-//
-// Read subsampling and strand inferring options
-//
-
-process {
-    withName: 'FQ_SUBSAMPLE' {
-        ext.args   = '--record-count 1000000 --seed 1'
-        ext.prefix = { "${meta.id}.subsampled" }
-        publishDir = [
-            enabled: false
-        ]
-    }
-
-    withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
-        ext.args   = '--skipQuant'
-        publishDir = [
-            enabled: false
-        ]
-    }
-}
-
-//
-// Read QC and trimming options
-//
-
-if (!(params.skip_fastqc || params.skip_qc)) {
-    if (params.trimmer == 'trimgalore') {
-        process {
-            withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
-                ext.args   = '--quiet'
-            }
-        }
-    }
-
-    if (params.trimmer == 'fastp') {
-        process {
-            withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
-                ext.args   = '--quiet'
-            }
-
-            withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
-                ext.args   = '--quiet'
-                publishDir = [
-                    path: { "${params.outdir}/${params.trimmer}/fastqc" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-}
-
-if (!params.skip_trimming) {
-    if (params.trimmer == 'trimgalore') {
-        process {
-            withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE' {
-                ext.args   = {
-                    [
-                        "--fastqc_args '-t ${task.cpus}'",
-                        params.extra_trimgalore_args ? params.extra_trimgalore_args.split("\\s(?=--)") : ''
-                    ].flatten().unique(false).join(' ').trim()
-                }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.trimmer}/fastqc" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.{html,zip}"
-                    ],
-                    [
-                        path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.fq.gz",
-                        saveAs: { params.save_trimmed ? it : null }
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.trimmer}" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.txt"
-                    ]
-                ]
-            }
-        }
-    }
-
-    if (params.trimmer == 'fastp') {
-        process {
-            withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
-                ext.args   = { params.extra_fastp_args ?: '' }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.trimmer}" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.{json,html}"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.trimmer}/log" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.log"
-                    ],
-                    [
-                        path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.fastq.gz",
-                        saveAs: { params.save_trimmed ? it : null }
-                    ]
-                ]
-            }
-        }
-    }
-}
-
-if (params.with_umi && !params.skip_umi_extract) {
-    process {
-        withName: 'UMITOOLS_EXTRACT' {
-            ext.args   = { [
-                    params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
-                    params.umitools_bc_pattern     ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
-                    params.umitools_bc_pattern2    ? "--bc-pattern2='${params.umitools_bc_pattern2}'" : '',
-                    params.umitools_umi_separator  ? "--umi-separator='${params.umitools_umi_separator}'" : ''
-            ].join(' ').trim() }
-            publishDir = [
-                [
-                    path: { "${params.outdir}/umitools" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.log"
-                ],
-                [
-                    path: { params.save_umi_intermeds ? "${params.outdir}/umitools" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz",
-                    saveAs: { params.save_umi_intermeds ? it : null }
-                ]
-            ]
-        }
-    }
-}
-
-//
-// Contaminant removal options
-//
-
-if (!params.skip_bbsplit) {
-    process {
-        withName: 'BBMAP_BBSPLIT' {
-            ext.args   = 'build=1 ambiguous2=all maxindel=150000'
-            publishDir = [
-                [
-                    path: { "${params.outdir}/bbsplit" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.txt'
-                ],
-                [
-                    path: { params.save_bbsplit_reads ? "${params.outdir}/bbsplit" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.fastq.gz',
-                    saveAs: { params.save_bbsplit_reads ? it : null }
-                ]
-            ]
-        }
-    }
-}
-
-if (params.remove_ribo_rna) {
-    process {
-        withName: 'SORTMERNA' {
-            ext.args   = '--num_alignments 1 -v'
-            publishDir = [
-                [
-                    path: { "${params.outdir}/sortmerna" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.log"
-                ],
-                [
-                    path: { params.save_non_ribo_reads ? "${params.outdir}/sortmerna" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz",
-                    saveAs: { params.save_non_ribo_reads ? it : null }
-                ]
-            ]
-        }
-    }
-}
-
-//
-// General alignment options
-//
-
-if (!params.skip_alignment) {
-    process {
-        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
-            ext.prefix = { "${meta.id}.sorted.bam" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                mode: params.publish_dir_mode,
-                pattern: "*.{stats,flagstat,idxstats}"
-            ]
-        }
-
-        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
-            ext.prefix = { "${meta.id}.sorted" }
-            publishDir = [
-                path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
-                    ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
-                mode: params.publish_dir_mode,
-                pattern: "*.bam",
-                saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
-                    ) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
-            ]
-        }
-
-        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
-            ext.args   = { params.bam_csi_index ? '-c' : '' }
-            publishDir = [
-                path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
-                    ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
-                mode: params.publish_dir_mode,
-                pattern: "*.{bai,csi}",
-                saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
-                    ) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
-            ]
-        }
-    }
-
-    if (!params.skip_markduplicates && !params.with_umi) {
-        process {
-            withName: '.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
-                ext.args   = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
-                ext.prefix = { "${meta.id}.markdup.sorted" }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/picard_metrics" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*metrics.txt'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam'
-                    ]
-                ]
-            }
-
-            withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
-                ext.args   = { params.bam_csi_index ? '-c' : '' }
-                ext.prefix = { "${meta.id}.markdup.sorted" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{bai,csi}'
-                ]
-            }
-
-            withName: '.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
-                ext.prefix = { "${meta.id}.markdup.sorted.bam" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
-            }
-        }
-    }
-
-    if (params.with_umi && ['star_salmon','hisat2'].contains(params.aligner)) {
-        process {
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
-                ext.args   = { [
-                    meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
-                    params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
-                    params.umitools_umi_separator   ? "--umi-separator='${params.umitools_umi_separator}'" : ''
-                ].join(' ').trim() }
-                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/umitools" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.tsv'
-                    ],
-                    [
-                        path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam',
-                        saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
-                    ]
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
-                ext.args   = { params.bam_csi_index ? '-c' : '' }
-                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
-                publishDir = [
-                    path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{bai,csi}',
-                    saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
-                ext.prefix = { "${meta.id}.umi_dedup.sorted.bam" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_bigwig) {
-        process {
-            withName: 'BEDTOOLS_GENOMECOV' {
-                ext.args   = '-split -du'
-                publishDir = [
-                    enabled: false
-                ]
-            }
-
-            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
-                ext.prefix = { "${meta.id}.clip.forward" }
-                publishDir = [
-                    enabled: false
-                ]
-            }
-
-            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
-                ext.prefix = { "${meta.id}.forward" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/bigwig" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-
-            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP' {
-                ext.prefix = { "${meta.id}.clip.reverse" }
-                publishDir = [
-                    enabled: false
-                ]
-            }
-
-            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
-                ext.prefix = { "${meta.id}.reverse" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/bigwig" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_stringtie) {
-        process {
-            withName: 'STRINGTIE_STRINGTIE' {
-                ext.args   = { [
-                    '-v',
-                    params.stringtie_ignore_gtf ? '' : '-e'
-                ].join(' ').trim() }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/stringtie" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-}
-
-//
-// STAR Salmon alignment options
-//
-
-if (!params.skip_alignment && params.aligner == 'star_salmon') {
-    process {
-        withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
-            ext.args   = { [
-                '--quantMode TranscriptomeSAM',
-                '--twopassMode Basic',
-                '--outSAMtype BAM Unsorted',
-                '--readFilesCommand zcat',
-                '--runRNGseed 0',
-                '--outFilterMultimapNmax 20',
-                '--alignSJDBoverhangMin 1',
-                '--outSAMattributes NH HI AS NM MD',
-                '--quantTranscriptomeBan Singleend',
-                '--outSAMstrandField intronMotif',
-                params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
-                params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : ''
-            ].flatten().unique(false).join(' ').trim() }
-            publishDir = [
-                [
-                    path: { "${params.outdir}/${params.aligner}/log" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{out,tab}'
-                ],
-                [
-                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bam',
-                    saveAs: { params.save_align_intermeds ? it : null }
-                ],
-                [
-                    path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.fastq.gz',
-                    saveAs: { params.save_unaligned ? it : null }
-                ]
-            ]
-        }
-
-        withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
-            ext.args   = { params.extra_salmon_quant_args ?: '' }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_STAR_SALMON:TX2GENE' {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_STAR_SALMON:TXIMPORT' {
-            ext.prefix = { "${quant_type}.merged" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_STAR_SALMON:SE_.*' {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-
-    if (params.with_umi) {
-        process {
-            withName: 'NFCORE_RNASEQ:RNASEQ:SAMTOOLS_SORT' {
-                ext.args   = '-n'
-                ext.prefix = { "${meta.id}.umi_dedup.transcriptome" }
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bam',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
-            }
-
-            withName: 'NFCORE_RNASEQ:RNASEQ:UMITOOLS_PREPAREFORSALMON' {
-                ext.prefix = { "${meta.id}.umi_dedup.transcriptome.filtered" }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/umitools/log" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.log'
-                    ],
-                    [
-                        path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam',
-                        saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                    ]
-                ]
-            }
-
-            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
-                ext.prefix = { "${meta.id}.transcriptome.sorted" }
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bam',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
-            }
-
-            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bai',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
-            }
-
-            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
-                ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}/samtools_stats" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
-                ext.args   = { [
-                    meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
-                    params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
-                    params.umitools_umi_separator   ? "--umi-separator='${params.umitools_umi_separator}'" : ''
-                ].join(' ').trim() }
-                ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/umitools" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.tsv'
-                    ],
-                    [
-                        path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam',
-                        saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                    ]
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bai',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
-                ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_qc & !params.skip_deseq2_qc) {
-        process {
-            withName: 'DESEQ2_QC_STAR_SALMON' {
-                ext.args   = { [
-                    "--id_col 1",
-                    "--sample_suffix ''",
-                    "--count_col 3",
-                    params.deseq2_vst ? '--vst TRUE' : ''
-                ].join(' ').trim() }
-                ext.args2  = 'star_salmon'
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
-                ]
-            }
-        }
-    }
-}
-
-//
-// STAR RSEM alignment options
-//
-
-if (!params.skip_alignment && params.aligner == 'star_rsem') {
-    process {
-        withName: '.*:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION' {
-            ext.args   = [
-                '--star',
-                '--star-output-genome-bam',
-                '--star-gzipped-read-file',
-                '--estimate-rspd',
-                '--seed 1'
-            ].join(' ').trim()
-            publishDir = [
-                [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.{stat,results}"
-                ],
-                [
-                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.bam",
-                    saveAs: { params.save_align_intermeds ? it : null }
-                ],
-                [
-                    path: { "${params.outdir}/${params.aligner}/log" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.log"
-                ]
-            ]
-        }
-
-        withName: '.*:QUANTIFY_RSEM:RSEM_MERGE_COUNTS' {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-
-    if (!params.skip_qc & !params.skip_deseq2_qc) {
-        process {
-            withName: 'DESEQ2_QC_RSEM' {
-                ext.args   = { [
-                    "--id_col 1",
-                    "--sample_suffix ''",
-                    "--count_col 3",
-                    params.deseq2_vst ? '--vst TRUE' : ''
-                ].join(' ').trim() }
-                ext.args2  = 'star_rsem'
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
-                ]
-            }
-        }
-    }
-}
-
-//
-// HISAT2 alignment options
-//
-
-if (!params.skip_alignment && params.aligner == 'hisat2') {
-    process {
-        withName: '.*:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN' {
-            ext.args   = '--met-stderr --new-summary --dta'
-            publishDir = [
-                [
-                    path: { "${params.outdir}/${params.aligner}/log" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.log'
-                ],
-                [
-                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bam',
-                    saveAs: { params.save_align_intermeds ? it : null }
-                ],
-                [
-                    path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.fastq.gz',
-                    saveAs: { params.save_unaligned ? it : null }
-                ]
-            ]
-        }
-    }
-}
-
-//
-// Post-alignment QC options
-//
-
-if (!params.skip_alignment && !params.skip_qc) {
-    if (!params.skip_preseq) {
-        process {
-            withName: 'PRESEQ_LCEXTRAP' {
-                ext.args   = '-verbose -bam -seed 1 -seg_len 100000000'
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/preseq" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.txt"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/preseq/log" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.log"
-                    ]
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_qualimap) {
-        process {
-            withName: 'QUALIMAP_RNASEQ' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/qualimap" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_dupradar) {
-        process {
-            withName: 'DUPRADAR' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/scatter_plot" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*Dens.pdf"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/box_plot" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*Boxplot.pdf"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/histogram" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*Hist.pdf"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/gene_data" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*Matrix.txt"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/intercepts_slope" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*slope.txt"
-                    ]
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_biotype_qc && params.featurecounts_group_type) {
-        process {
-            withName: 'SUBREAD_FEATURECOUNTS' {
-                ext.args   = { [
-                    '-B -C',
-                    params.gencode ? "-g gene_type" : "-g $params.featurecounts_group_type",
-                    "-t $params.featurecounts_feature_type"
-                ].join(' ').trim() }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-
-            withName: 'MULTIQC_CUSTOM_BIOTYPE' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_rseqc && 'bam_stat' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_BAMSTAT' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_rseqc && 'infer_experiment' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_rseqc && 'junction_annotation' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/pdf" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.pdf'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/bed" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bed'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/xls" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.xls'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/log" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.log'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/rscript" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.r'
-                    ]
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_rseqc && 'junction_saturation' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONSATURATION' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/pdf" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.pdf'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/rscript" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.r'
-                    ]
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_rseqc && 'read_duplication' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_READDUPLICATION' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/pdf" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.pdf'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/xls" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.xls'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/rscript" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.r'
-                    ]
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_rseqc && 'read_distribution' in rseqc_modules && !params.bam_csi_index) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_READDISTRIBUTION' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_rseqc && 'inner_distance' in rseqc_modules && !params.bam_csi_index) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_INNERDISTANCE' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.txt',
-                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/pdf" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.pdf'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/rscript" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.r'
-                    ]
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_rseqc && 'tin' in rseqc_modules && !params.bam_csi_index) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_TIN' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-}
-
-if (!params.skip_multiqc) {
-    process {
-        withName: 'MULTIQC' {
-            ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-            ext.prefix = "multiqc_report"
-            publishDir = [
-                path: { [
-                    "${params.outdir}/multiqc",
-                    params.skip_alignment? '' : "/${params.aligner}"
-                    ].join('') },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-}
-
-//
-// Salmon/ Kallisto pseudoalignment options
-//
-
-if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
-    process {
-        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT' {
-            ext.args   = { params.extra_salmon_quant_args ?: '' }
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
-            ]
-        }
-    }
-}
-
-if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') {
-    process {
-        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:KALLISTO_QUANT' {
-            ext.args = params.extra_kallisto_quant_args ?: ''
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.run_info.json') || filename.endsWith('.log') ? null : filename }
-            ]
-        }
-    }
-}
-
-if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
-    process {
-        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE' {
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMPORT' {
-            ext.prefix = { "${quant_type}.merged" }
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*' {
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-
-    if (!params.skip_qc & !params.skip_deseq2_qc) {
-        process {
-            withName: 'DESEQ2_QC_PSEUDO' {
-                ext.args   = { [
-                    "--id_col 1",
-                    "--sample_suffix ''",
-                    "--count_col 3",
-                    params.deseq2_vst ? '--vst TRUE' : ''
-                ].join(' ').trim() }
-                ext.args2  = { params.pseudo_aligner }
-                publishDir = [
-                    path: { "${params.outdir}/${params.pseudo_aligner}/deseq2_qc" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
-                ]
-            }
-        }
-    }
-}
diff --git a/conf/test.config b/conf/test.config
index f9154ba31..f7a9fca91 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -19,21 +19,20 @@ params {
     max_memory = '6.GB'
     max_time   = '6.h'
 
-
     // Input data
-    input = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv"
+    input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv'
 
     // Genome references
-    fasta              = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta"
-    gtf                = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz"
-    gff                = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes.gff.gz"
-    transcript_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/transcriptome.fasta"
-    additional_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz"
-
-    bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txt"
-    hisat2_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/hisat2.tar.gz"
-    salmon_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gz"
-    rsem_index         = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/rsem.tar.gz"
+    fasta              = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta'
+    gtf                = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz'
+    gff                = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz'
+    transcript_fasta   = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta'
+    additional_fasta   = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz'
+
+    bbsplit_fasta_list = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt'
+    hisat2_index       = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz'
+    salmon_index       = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz'
+    rsem_index         = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz'
 
     // Other parameters
     skip_bbsplit        = false
diff --git a/conf/test_cache.config b/conf/test_cache.config
deleted file mode 100644
index 51aad577e..000000000
--- a/conf/test_cache.config
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests using cached / offline test data
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run nf-core/rnaseq -profile test,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
-
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
-
-    // Input data
-    // params.test_data_base (default) = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/'
-    input = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv"
-
-    // Genome references
-    fasta              = "${params.test_data_base}/reference/genome.fasta"
-    gtf                = "${params.test_data_base}/reference/genes.gtf.gz"
-    gff                = "${params.test_data_base}/reference/genes.gff.gz"
-    transcript_fasta   = "${params.test_data_base}/reference/transcriptome.fasta"
-    additional_fasta   = "${params.test_data_base}/reference/gfp.fa.gz"
-
-    bbsplit_fasta_list = "${params.test_data_base}/reference/bbsplit_fasta_list.txt"
-    hisat2_index       = "${params.test_data_base}/reference/hisat2.tar.gz"
-    salmon_index       = "${params.test_data_base}/reference/salmon.tar.gz"
-    rsem_index         = "${params.test_data_base}/reference/rsem.tar.gz"
-
-    // Other parameters
-    skip_bbsplit        = false
-    pseudo_aligner      = 'salmon'
-    umitools_bc_pattern = 'NNNN'
-}
-
-// When using RSEM, remove warning from STAR whilst building tiny indices
-process {
-    withName: 'RSEM_PREPAREREFERENCE_GENOME' {
-        ext.args2 = "--genomeSAindexNbases 7"
-    }
-}
diff --git a/conf/test_full.config b/conf/test_full.config
index d63a1f676..320b8156f 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Parameters for full-size test
-    input          = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_full.csv'
+    input          = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_full.csv'
     genome         = 'GRCh37'
     pseudo_aligner = 'salmon'
 }
diff --git a/docs/images/mqc_strand_check.png b/docs/images/mqc_strand_check.png
old mode 100755
new mode 100644
index 7b163f9ea..54ae2f275
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diff --git a/docs/images/nf-core-rnaseq_logo_dark.png b/docs/images/nf-core-rnaseq_logo_dark.png
index ff8abdd96..a13319659 100644
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diff --git a/docs/images/nf-core-rnaseq_logo_light.png b/docs/images/nf-core-rnaseq_logo_light.png
index b0c99cb83..c156a0a0a 100644
Binary files a/docs/images/nf-core-rnaseq_logo_light.png and b/docs/images/nf-core-rnaseq_logo_light.png differ
diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.png b/docs/images/nf-core-rnaseq_metro_map_grey.png
index 0dbf23f81..d2c040315 100644
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diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.svg b/docs/images/nf-core-rnaseq_metro_map_grey.svg
index b17e5844c..7b55ae7e5 100644
--- a/docs/images/nf-core-rnaseq_metro_map_grey.svg
+++ b/docs/images/nf-core-rnaseq_metro_map_grey.svg
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diff --git a/docs/output.md b/docs/output.md
index a4c559b3b..bb2f03f6b 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -367,7 +367,7 @@ The majority of RSeQC scripts generate output files which can be plotted and sum
 
 </details>
 
-This script predicts the "strandedness" of the protocol (i.e. unstranded, sense or antisense) that was used to prepare the sample for sequencing by assessing the orientation in which aligned reads overlay gene features in the reference genome. The strandedness of each sample has to be provided to the pipeline in the input samplesheet (see [usage docs](https://nf-co.re/rnaseq/usage#samplesheet-input)). However, this information is not always available, especially for public datasets. As a result, additional features have been incorporated into this pipeline to auto-detect whether you have provided the correct information in the samplesheet, and if this is not the case then a warning table will be placed at the top of the MultiQC report highlighting the offending samples (see image below). If required, this will allow you to correct the input samplesheet and rerun the pipeline with the accurate strand information. Note, it is important to get this information right because it can affect the final results.
+This script predicts the "strandedness" of the protocol (i.e. unstranded, sense or antisense) that was used to prepare the sample for sequencing by assessing the orientation in which aligned reads overlay gene features in the reference genome. The strandedness of each sample has to be provided to the pipeline in the input samplesheet (see [usage docs](https://nf-co.re/rnaseq/usage#samplesheet-input)). However, this information is not always available, especially for public datasets. As a result, additional features have been incorporated into this pipeline to auto-detect whether you have provided the correct information in the samplesheet, and if this is not the case then the affected libraries will be flagged in the table under 'Strandedness Checks' elsewhere in the report. If required, this will allow you to correct the input samplesheet and rerun the pipeline with the accurate strand information. Note, it is important to get this information right because it can affect the final results.
 
 RSeQC documentation: [infer_experiment.py](http://rseqc.sourceforge.net/#infer-experiment-py)
 
@@ -642,6 +642,8 @@ The script included in the pipeline uses DESeq2 to normalise read counts across
 
 By default, the pipeline uses the `vst` transformation which is more suited to larger experiments. You can set the parameter `--deseq2_vst false` if you wish to use the DESeq2 native `rlog` option. See [DESeq2 docs](http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-transformations-and-visualization) for a more detailed explanation.
 
+Both types of transformation are performed blind, i.e. using across-all-samples variability, without using any prior information on experimental groups (equivalent to using an intercept-only design), as recommended by the [DESeq2 docs](https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#blind-dispersion-estimation).
+
 The PCA plots are generated based alternately on the top five hundred most variable genes, or all genes. The former is the conventional approach that is more likely to pick up strong effects (ie the biological signal) and the latter, when different, is picking up a weaker but consistent effect that is synchronised across many transcripts. We project both of these onto the first two PCs (shown in the top row of the figure below), which is the best two dimensional representation of the variation between samples.
 
 We also explore higher components in terms of experimental factors inferred from sample names. If your sample naming convention follows a strict policy of using underscores to delimit values of experimental factors (for example `WT_UNTREATED_REP1`) and all names have the same number of underscores (so excluding `WT_TREATED_10ml_REP1` from being compatible with the previous label), then any of these factors that are informative (ie label some but not all samples the same) then we individually plot upto the first five PCs, per experimental level, for each of the experimental factors.
@@ -682,9 +684,10 @@ The principal output files are the same between Salmon and Kallsto:
   - `<pseudo_aligner>.merged.gene_counts.tsv`: Matrix of gene-level raw counts across all samples.
   - `<pseudo_aligner>.gene_tpm.tsv`: Matrix of gene-level TPM values across all samples.
   - `<pseudo_aligner>.gene_counts.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the TPM (`abundance`), estimated counts (`counts`) and transcript length (`length`) in the assays slot for genes.
-  - `<pseudo_aligner>.merged.gene_counts_scaled.tsv`: Matrix of gene-level library size-scaled counts across all samples.
+  - `<pseudo_aligner>.merged.gene_lengths.tsv`: Matrix of average within-sample transcript lengths for each gene across all samples.
+  - `<pseudo_aligner>.merged.gene_counts_scaled.tsv`: Matrix of gene-level library size-scaled estimated counts across all samples.
   - `<pseudo_aligner>.merged.gene_counts_scaled.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the TPM (`abundance`), estimated library size-scaled counts (`counts`) and transcript length (`length`) in the assays slot for genes.
-  - `<pseudo_aligner>.merged.gene_counts_length_scaled.tsv`: Matrix of gene-level length-scaled counts across all samples.
+  - `<pseudo_aligner>.merged.gene_counts_length_scaled.tsv`: Matrix of gene-level length-scaled estimated counts across all samples.
   - `<pseudo_aligner>.merged.gene_counts_length_scaled.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the TPM (`abundance`), estimated length-scaled counts (`counts`) and transcript length (`length`) in the assays slot for genes.
   - `<pseudo_aligner>.merged.transcript_counts.tsv`: Matrix of isoform-level raw counts across all samples.
   - `<pseudo_aligner>.merged.transcript_tpm.tsv`: Matrix of isoform-level TPM values across all samples.
@@ -725,11 +728,11 @@ Transcripts with large inferential uncertainty won't be assigned the exact numbe
 
 The [tximport](https://bioconductor.org/packages/release/bioc/html/tximport.html) package is used in this pipeline to summarise the results generated by Salmon or Kallisto into matrices for use with downstream differential analysis packages. We use tximport with different options to summarize count and TPM quantifications at the gene- and transcript-level. Please see [#499](https://github.com/nf-core/rnaseq/issues/499) for discussion and links regarding which counts are suitable for different types of analysis.
 
-According to the `txtimport` documentation you can do one of the following:
+According to the [`txtimport` documentation](https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Downstream_DGE_in_Bioconductor) you can do one of the following:
 
-- Use bias corrected counts with an offset: import all the salmon files with `tximport` and then use `DESeq2` with `dds <- DESeqDataSetFromTximport(txi, sampleTable, ~condition)` to correct for changes to the average transcript length across samples.
-- Use bias corrected counts without an offset: load and use `salmon.merged.gene_counts_length_scaled.tsv` or `salmon.merged.gene_counts_scaled.tsv` directly as you would with a regular counts matrix.
-- Use bias uncorrected counts: load and use the `txi$counts` matrix (or `salmon.merged.gene_counts.tsv`) with `DESeq2`. This does not correct for potential differential isoform usage. Alternatively, if you have 3’ tagged RNA-seq data this is the most suitable method.
+- Use the original (bias-uncorrected) counts _with an offset_: import all the salmon `quant.sf` files with `tximport` and then use `DESeq2` with `dds <- DESeqDataSetFromTximport(txi, sampleTable, ~condition)` to automatically construct an object with gene-level offsets in-built, which can be used by DESeq2 to automatically account for effective gene length effects across conditions. It's also possible to combine the `.merged.gene_counts.tsv` and `.gene_lengths.tsv` matrices output by this workflow to make your own object the same way - which is what [the nf-core differentialabundance workflow does](https://nf-co.re/differentialabundance/1.5.0/docs/usage#outputs-from-nf-corernaseq-and-other-tximport-processed-results). See the [DESeq2 module](https://github.com/nf-core/modules/blob/c8f7f481bf2ccd8f9c7f2d499d94e74d4b9e23ab/modules/nf-core/deseq2/differential/templates/deseq_de.R#L323) for the implementation details.
+- Use bias-corrected counts _without an offset_: load and use `salmon.merged.gene_counts_length_scaled.tsv` or `salmon.merged.gene_counts_scaled.tsv` directly as you would with a regular gene-level counts matrix. These files were created using the `tximport` argument `countsFromAbundance="scaledTPM"` or `"lengthScaledTPM"` to scale counts to library size or to library size and average transcript length respectively.
+- Use the original (bias-uncorrected) counts _without an offset_: load and use the `txi$counts` matrix (or `salmon.merged.gene_counts.tsv`) with `DESeq2`. This is generally **not** recommended, since it does not correct for potential differential isoform usage (the offset). However, if you have 3’ tagged RNA-seq data, then this _is_ the most suitable method, because the counts do not exhibit any length bias.
 
 > **NB:** The default Salmon parameters and a k-mer size of 31 are used to create the index. As [documented here](https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode) and [discussed here](https://github.com/COMBINE-lab/salmon/issues/482#issuecomment-583799668), a k-mer size off 31 works well with reads that are 75bp or longer.
 
diff --git a/docs/usage.md b/docs/usage.md
index 7b148c636..b613ab79d 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -18,7 +18,7 @@ You will need to create a samplesheet with information about the samples you wou
 
 ### Multiple runs of the same sample
 
-The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes. If you set the strandedness value to `auto` the pipeline will sub-sample the input FastQ files to 1 million reads, use Salmon Quant to infer the strandedness automatically and then propagate this information to the remainder of the pipeline. If the strandedness has been inferred or provided incorrectly a warning will be present at the top of the MultiQC report so please be sure to check when looking at the QC for your samples.
+The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes.
 
 ```csv title="samplesheet.csv"
 sample,fastq_1,fastq_2,strandedness
@@ -27,6 +27,51 @@ CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,a
 CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,auto
 ```
 
+### Strandedness Prediction
+
+If you set the strandedness value to `auto`, the pipeline will sub-sample the input FastQ files to 1 million reads, use Salmon Quant to automatically infer the strandedness, and then propagate this information through the rest of the pipeline. This behavior is controlled by the `--stranded_threshold` and `--unstranded_threshold` parameters, which are set to 0.8 and 0.1 by default, respectively. This means:
+
+- **Forward stranded:** At least 80% of the fragments are in the 'forward' orientation.
+- **Unstranded:** The forward and reverse fractions differ by less than 10%.
+- **Undetermined:** Samples that do not meet either criterion, possibly indicating issues such as genomic DNA contamination.
+
+**Note:** These thresholds apply to both the strandedness inferred from Salmon outputs for input to the pipeline and how strandedness is inferred from RSeQC results using pipeline outputs.
+
+#### Usage Examples
+
+1. **Forward Stranded Sample:**
+
+   - Forward fraction: 0.85
+   - Reverse fraction: 0.15
+   - **Classification:** Forward stranded
+
+2. **Reverse Stranded Sample:**
+
+   - Forward fraction: 0.1
+   - Reverse fraction: 0.9
+   - **Classification:** Reverse stranded
+
+3. **Unstranded Sample:**
+
+   - Forward fraction: 0.45
+   - Reverse fraction: 0.55
+   - **Classification:** Unstranded
+
+4. **Undetermined Sample:**
+   - Forward fraction: 0.6
+   - Reverse fraction: 0.4
+   - **Classification:** Undetermined
+
+You can control the stringency of this behavior with `--stranded_threshold` and `--unstranded_threshold`.
+
+#### Errors and Reporting
+
+The results of strandedness inference are displayed in the MultiQC report under 'Strandedness Checks'. This shows any provided strandedness and the results inferred by both Salmon (when strandedness is set to 'auto') and RSeQC. Mismatches between input strandedness (explicitly provided by the user or inferred by Salmon) and output strandedness from RSeQC are marked as fails. For example, if a user specifies 'forward' as strandedness for a library that is actually reverse stranded, this is marked as a fail.
+
+![MultiQC - Strand check table](images/mqc_strand_check.png)
+
+Be sure to check the strandedness report when reviewing the QC for your samples.
+
 ### Full samplesheet
 
 The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 4 columns to match those defined in the table below.
@@ -55,6 +100,14 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 
 > **NB:** The `group` and `replicate` columns were replaced with a single `sample` column as of v3.1 of the pipeline. The `sample` column is essentially a concatenation of the `group` and `replicate` columns, however it now also offers more flexibility in instances where replicate information is not required e.g. when sequencing clinical samples. If all values of `sample` have the same number of underscores, fields defined by these underscore-separated names may be used in the PCA plots produced by the pipeline, to regain the ability to represent different groupings.
 
+## FASTQ sampling
+
+If you would like to reduce the number of reads used in the analysis, for example to test pipeline operation with limited resource usage, you can make use of the FASTP option for trimming (see below). FASTP has an option to take the first `n` reads of input FASTQ file(s), so this can be used to reduce the reads passed to subsequent steps. For example, to pass only the first 10,000 reads for trimming you would set input paramters like:
+
+```
+--trimmer fastp --extra_fastp_args '--reads_to_process 10000'
+```
+
 ## Adapter trimming options
 
 [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) is a wrapper tool around Cutadapt and FastQC to peform quality and adapter trimming on FastQ files. Trim Galore! will automatically detect and trim the appropriate adapter sequence. It is the default trimming tool used by this pipeline, however you can use fastp instead by specifying the `--trimmer fastp` parameter. [fastp](https://github.com/OpenGene/fastp) is a tool designed to provide fast, all-in-one preprocessing for FastQ files. It has been developed in C++ with multithreading support to achieve higher performance. You can specify additional options for Trim Galore! and fastp via the `--extra_trimgalore_args` and `--extra_fastp_args` parameters, respectively.
@@ -93,12 +146,13 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic
 
 #### Examples:
 
-| UMI type     | Source                                                                                                                                                                                                                                               | Pipeline parameters                                                                                                                            |
-| ------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------- |
-| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf)                                      | `--with_umi --skip_umi_extract --umitools_umi_separator ":"`                                                                                   |
-| In sequence  | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries)                                          | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{6})(?P<discard_1>.{4}).*"`                                   |
-| In sequence  | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)<br> > _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_       | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{12}).*"`<br>Optional: `--clip_r2 9 --three_prime_clip_r2 12` |
-| In sequence  | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*"`                                  |
+| UMI type     | Source                                                                                                                                                                                                                                                                                                                              | Pipeline parameters                                                                                                                                                         |
+| ------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf)                                                                                                                     | `--with_umi --skip_umi_extract --umitools_umi_separator ":"`                                                                                                                |
+| In sequence  | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries)                                                                                                                         | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{6})(?P<discard_1>.{4}).*"`                                                                |
+| In sequence  | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)<br> > _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_                                                                                      | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{12}).*"`<br>Optional: `--clip_r2 9 --three_prime_clip_r2 12`                              |
+| In sequence  | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf)                                                                                | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*"`                                                               |
+| In sequence  | [Watchmaker mRNA Library Prep Kit](https://watchmakergenomics.com/wp-content/uploads/2023/11/M223_mRNA-Library-Prep-Kit-_UG_WMUG214_v1-1-0823.pdf) with [Twist UMI Adapter System](https://www.twistbioscience.com/sites/default/files/resources/2023-03/DOC-001337_TechNote-ProcessingSequencingDataUtilizingUMI-REV1-singles.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{5})(?P<discard_1>.{2}).*" --umitools_bc_pattern2 "^(?P<umi_2>.{5})(?P<discard_2>.{2}).*"` |
 
 > _No warranty for the accuracy or completeness of the parameters is implied_
 
@@ -137,6 +191,12 @@ If unique molecular identifiers were used to prepare the library, add the follow
 
 Please refer to the [nf-core website](https://nf-co.re/usage/reference_genomes) for general usage docs and guidelines regarding reference genomes.
 
+:::note
+**Consistent reference resource usage**
+
+When supplying reference files as discussed below, it is important to be consistent in the reference resource used (Ensembl, GENCODE, UCSC etc), since differences in conventions between these resources can make their files incompatible. For example, UCSC prefixes chromosomes with `chr`, while Ensembl does not, so a GTF file from Ensembl should not be supplied alongside a genome FASTA from UCSC. GENCODE also attaches version identifiers to gene and transcript names (e.g. `ENSG00000254647.1`) while Ensembl does not.
+:::
+
 ### Explicit reference file specification (recommended)
 
 The minimum reference genome requirements for this pipeline are a FASTA and GTF file, all other files required to run the pipeline can be generated from these files. For example, the latest reference files for human can be derived from Ensembl like:
@@ -158,6 +218,36 @@ Notes:
 - If `--additional_fasta` is provided then the features in this file (e.g. ERCC spike-ins) will be automatically concatenated onto both the reference FASTA file as well as the GTF annotation before building the appropriate indices.
 - When using `--aligner star_rsem`, both the STAR and RSEM indices should be present in the path specified by `--rsem_index` (see [#568](https://github.com/nf-core/rnaseq/issues/568)).
 
+#### Reference genome
+
+It is recommended to provide the most complete reference genome for your species, without additional loci (haplotypes) or patches. For model organisms such as mouse or human, this is the "primary assembly", which includes the reference chromosomes and some additional scaffolds. For the human assembly GRCh38 (hg38), use the `GRCh38.primary_assembly.genome.fa.gz` file from GENCODE or the `Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz` file from Ensembl. These files cover the largest portion of the reference genome without including multiple copies of the same sequence, which would result in heavy mapping quality penalties.
+
+For most other species (e.g., fly, cow, dog), no primary assembly is published. This reflects inadequately characterized genomic variation and a lower degree of curation, meaning that there are no established alternative loci (haplotypes), and that the toplevel file is equivalent to a primary assembly. Therefore, while the toplevel assembly may be utilized for these organisms, it is nonetheless advisable to verify the absence of N-padded haplotype or patch regions first.
+
+#### Gene annotation
+
+Gene annotations are updated more frequently than the reference genome sequence, so you must choose an appropriate annotation version (e.g. Ensembl release). We recommend using sources with well-defined, versioned releases such as ENSEMBL or GENCODE. Generally, it is best to use the most recent release for the latest gene annotations. However, if you are combining your data with older datasets, use the annotation version previously used for consistency.
+
+Once you have chosen a release, select the annotation file that matches your reference genome. For the human primary assembly, use the comprehensive annotation (e.g., `gencode.{release}.primary_assembly.annotation.gtf.gz` from GENCODE or `Homo_sapiens.GRCh38.{release}.gtf.gz` from Ensembl). For other species, like fly, use the annotation matching the toplevel assembly (e.g., `Drosophila_melanogaster.BDGP6.46.{release}.gtf.gz` from Ensembl).
+
+Ensure that the annotation files use gene IDs as the primary identifier, not the gene name/symbol. For example, the Ensembl ID `ENSG00000254647` corresponds to the `INS` gene, which encodes the insulin protein. While gene names are more familiar, it is crucial to retain and use the primary identifiers as they are unique and easier to map between annotation versions or sources.
+
+To take advantage of all the quality control modules implemented in the pipeline, the gene annotation should include a `gene_biotype` field which describes the function of each feature (protein coding, long non-coding etc.). This is usually the case for annotations from GENCODE or Ensembl but may not be if your annotation comes from another source. If your annotation does not include this field, please set the `--skip_biotype_qc` option to avoid running the steps that rely on it.
+
+:::note
+**GTF vs GFF**
+
+GFF (General Feature Format) is a tab-separated text file format for representing genomic annotations, while GTF (General Transfer Format) is a specific implementation of this format corresponding to GFF version 2. The pipeline can accept both GFF and GTF but any GFF files will be converted to GTF so if a GTF is available for your annotation of choice it is better to provide that directly.
+
+More information and links to further resources are [available from Ensembl](https://www.ensembl.org/info/website/upload/gff.html).
+:::
+
+#### Reference transcriptome
+
+In addition to the reference genome sequence and annotation, you can provide a reference transcriptome FASTA file. These files can be obtained from GENCODE or Ensembl. However, these sequences only cover the reference chromosomes and can cause inconsistencies if you are using a primary or toplevel genome assembly and annotation.
+
+We recommend not providing a transcriptome FASTA file and instead allowing the pipeline to create it from the provided genome and annotation. Similar to aligner indexes, you can save the created transcriptome FASTA and BED files to a central location for future pipeline runs. This helps avoid redundant computation and having multiple copies on your system. Ensure that all genome, annotation, transcriptome, and index versions match to maintain consistency.
+
 #### Indices
 
 By default, indices are generated dynamically by the workflow for tools such as STAR and Salmon. Since indexing is an expensive process in time and resources you should ensure that it is only done once, by retaining the indices generated from each batch of reference files:
@@ -167,13 +257,17 @@ By default, indices are generated dynamically by the workflow for tools such as
 
 Once you have the indices from a workflow run you should save them somewhere central and reuse them in subsequent runs using custom config files or command line parameters such as `--star_index '/path/to/STAR/index/'`.
 
-#### Gencode
+Remember to note the genome and annotation versions as well as the versions of the software used for indexing, as an index created with one version may not be compatible with other versions.
+
+#### GENCODE
 
 If you are using [GENCODE](https://www.gencodegenes.org/) reference genome files please specify the `--gencode` parameter because the format of these files is slightly different to ENSEMBL genome files:
 
 - The `--gtf_group_features_type` parameter will automatically be set to `gene_type` as opposed to `gene_biotype`, respectively.
 - If you are running Salmon, the `--gencode` flag will also be passed to the index building step to overcome parsing issues resulting from the transcript IDs in GENCODE fasta files being separated by vertical pipes (`|`) instead of spaces (see [this issue](https://github.com/COMBINE-lab/salmon/issues/15)).
 
+As well as the standard annotations, GENCODE also provides "basic" annotations, which include only representative transcripts, but we do not recommend using these.
+
 #### Prokaryotic genome annotations
 
 This pipeline uses featureCounts to generate QC metrics based on [biotype](http://www.ensembl.org/info/genome/genebuild/biotypes.html) information available within GFF/GTF genome annotation files. The format of these annotation files can vary significantly depending on the source of the annotation and the type of organism. The default settings in the pipeline are tailored towards Ensembl GTF annotations available for eukaryotic genomes. Prokaryotic genome annotations tend to be distributed in GFF format which are structured differently in terms of the feature naming conventions. There are a number of ways you can tune the behaviour of the pipeline to cater for differences/absence of biotype information:
@@ -213,8 +307,6 @@ nextflow run \
     --outdir <OUTDIR> \
     --gtf <GTF> \
     --fasta <GENOME FASTA> \
-    --igenomes_ignore \
-    --genome null \
     -profile docker
 ```
 
@@ -316,6 +408,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `wave`
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
@@ -357,14 +451,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
-## Azure Resource Requests
-
-To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
-We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
-
-Note that the choice of VM size depends on your quota and the overall workload during the analysis.
-For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
-
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
deleted file mode 100755
index 5cdc9a73c..000000000
--- a/lib/NfcoreTemplate.groovy
+++ /dev/null
@@ -1,398 +0,0 @@
-//
-// This file holds several functions used within the nf-core pipeline template.
-//
-
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
-class NfcoreTemplate {
-
-    //
-    // Check AWS Batch related parameters have been specified correctly
-    //
-    public static void awsBatch(workflow, params) {
-        if (workflow.profile.contains('awsbatch')) {
-            // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
-            assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
-            // Check outdir paths to be S3 buckets if running on AWSBatch
-            assert params.outdir.startsWith('s3:')       : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
-        }
-    }
-
-    //
-    //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
-    //
-    public static void checkConfigProvided(workflow, log) {
-        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-                    "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-                    "Please refer to the quick start section and usage docs for the pipeline.\n "
-        }
-    }
-
-    //
-    //  Warn if using custom configs to provide pipeline parameters
-    //
-    public static void warnParamsProvidedInConfig(workflow, log) {
-        if (workflow.configFiles.size() > 1) {
-            log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                "  Multiple config files detected!\n" +
-                "  Please provide pipeline parameters via the CLI or Nextflow '-params-file' option.\n" +
-                "  Custom config files including those provided by the '-c' Nextflow option can be\n" +
-                "  used to provide any configuration except for parameters.\n\n" +
-                "  Docs: https://nf-co.re/usage/configuration#custom-configuration-files\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        }
-    }
-
-    //
-    // Generate version string
-    //
-    public static String version(workflow) {
-        String version_string = ""
-
-        if (workflow.manifest.version) {
-            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-            version_string += "${prefix_v}${workflow.manifest.version}"
-        }
-
-        if (workflow.commitId) {
-            def git_shortsha = workflow.commitId.substring(0, 7)
-            version_string += "-g${git_shortsha}"
-        }
-
-        return version_string
-    }
-
-    //
-    // Construct and send completion email
-    //
-    public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[], pass_mapped_reads=[:], pass_trimmed_reads=[:], pass_strand_check=[:]) {
-
-        // Set up the e-mail variables
-        def fail_mapped_count  = pass_mapped_reads.count  { key, value -> value == false }
-        def fail_trimmed_count = pass_trimmed_reads.count { key, value -> value == false }
-        def fail_strand_count  = pass_strand_check.count  { key, value -> value == false }
-
-        def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
-        if (fail_mapped_count + fail_trimmed_count + fail_strand_count > 0) {
-            subject = "[$workflow.manifest.name] Partially successful - samples skipped: $workflow.runName"
-        }
-        if (!workflow.success) {
-            subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
-        }
-
-        def summary = [:]
-        for (group in summary_params.keySet()) {
-            summary << summary_params[group]
-        }
-
-        def misc_fields = [:]
-        misc_fields['Date Started']              = workflow.start
-        misc_fields['Date Completed']            = workflow.complete
-        misc_fields['Pipeline script file path'] = workflow.scriptFile
-        misc_fields['Pipeline script hash ID']   = workflow.scriptId
-        if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-        if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-        if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-        misc_fields['Nextflow Version']           = workflow.nextflow.version
-        misc_fields['Nextflow Build']             = workflow.nextflow.build
-        misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
-
-        def email_fields = [:]
-        email_fields['version']      = NfcoreTemplate.version(workflow)
-        email_fields['runName']      = workflow.runName
-        email_fields['success']      = workflow.success
-        email_fields['dateComplete'] = workflow.complete
-        email_fields['duration']     = workflow.duration
-        email_fields['exitStatus']   = workflow.exitStatus
-        email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-        email_fields['errorReport']  = (workflow.errorReport ?: 'None')
-        email_fields['commandLine']  = workflow.commandLine
-        email_fields['projectDir']   = workflow.projectDir
-        email_fields['summary']      = summary << misc_fields
-        email_fields['skip_sample_count'] = fail_mapped_count + fail_trimmed_count + fail_strand_count
-
-        // On success try attach the multiqc report
-        def mqc_report = null
-        try {
-            if (workflow.success && !params.skip_multiqc) {
-                mqc_report = multiqc_report.getVal()
-                if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                    if (mqc_report.size() > 1) {
-                        log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
-                    }
-                    mqc_report = mqc_report[0]
-                }
-            }
-        } catch (all) {
-            if (multiqc_report) {
-                log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
-            }
-        }
-
-        // Check if we are only sending emails on failure
-        def email_address = params.email
-        if (!params.email && params.email_on_fail && !workflow.success) {
-            email_address = params.email_on_fail
-        }
-
-        // Render the TXT template
-        def engine       = new groovy.text.GStringTemplateEngine()
-        def tf           = new File("$projectDir/assets/email_template.txt")
-        def txt_template = engine.createTemplate(tf).make(email_fields)
-        def email_txt    = txt_template.toString()
-
-        // Render the HTML template
-        def hf            = new File("$projectDir/assets/email_template.html")
-        def html_template = engine.createTemplate(hf).make(email_fields)
-        def email_html    = html_template.toString()
-
-        // Render the sendmail template
-        def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
-        def sf                     = new File("$projectDir/assets/sendmail_template.txt")
-        def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
-        def sendmail_html          = sendmail_template.toString()
-
-        // Send the HTML e-mail
-        Map colors = logColours(params.monochrome_logs)
-        if (email_address) {
-            try {
-                if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
-                // Try to send HTML e-mail using sendmail
-                def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
-                sendmail_tf.withWriter { w -> w << sendmail_html }
-                [ 'sendmail', '-t' ].execute() << sendmail_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-            } catch (all) {
-                // Catch failures and try with plaintext
-                def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-                if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
-                    mail_cmd += [ '-A', mqc_report ]
-                }
-                mail_cmd.execute() << email_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
-            }
-        }
-
-        // Write summary e-mail HTML to a file
-        def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
-        output_hf.withWriter { w -> w << email_html }
-        FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html");
-        output_hf.delete()
-
-        // Write summary e-mail TXT to a file
-        def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
-        output_tf.withWriter { w -> w << email_txt }
-        FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt");
-        output_tf.delete()
-    }
-
-    //
-    // Construct and send a notification to a web server as JSON
-    // e.g. Microsoft Teams and Slack
-    //
-    public static void IM_notification(workflow, params, summary_params, projectDir, log) {
-        def hook_url = params.hook_url
-
-        def summary = [:]
-        for (group in summary_params.keySet()) {
-            summary << summary_params[group]
-        }
-
-        def misc_fields = [:]
-        misc_fields['start']                                = workflow.start
-        misc_fields['complete']                             = workflow.complete
-        misc_fields['scriptfile']                           = workflow.scriptFile
-        misc_fields['scriptid']                             = workflow.scriptId
-        if (workflow.repository) misc_fields['repository']  = workflow.repository
-        if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-        if (workflow.revision)   misc_fields['revision']    = workflow.revision
-        misc_fields['nxf_version']                          = workflow.nextflow.version
-        misc_fields['nxf_build']                            = workflow.nextflow.build
-        misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
-
-        def msg_fields = [:]
-        msg_fields['version']      = NfcoreTemplate.version(workflow)
-        msg_fields['runName']      = workflow.runName
-        msg_fields['success']      = workflow.success
-        msg_fields['dateComplete'] = workflow.complete
-        msg_fields['duration']     = workflow.duration
-        msg_fields['exitStatus']   = workflow.exitStatus
-        msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-        msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
-        msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
-        msg_fields['projectDir']   = workflow.projectDir
-        msg_fields['summary']      = summary << misc_fields
-
-        // Render the JSON template
-        def engine       = new groovy.text.GStringTemplateEngine()
-        // Different JSON depending on the service provider
-        // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
-        def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
-        def hf            = new File("$projectDir/assets/${json_path}")
-        def json_template = engine.createTemplate(hf).make(msg_fields)
-        def json_message  = json_template.toString()
-
-        // POST
-        def post = new URL(hook_url).openConnection();
-        post.setRequestMethod("POST")
-        post.setDoOutput(true)
-        post.setRequestProperty("Content-Type", "application/json")
-        post.getOutputStream().write(json_message.getBytes("UTF-8"));
-        def postRC = post.getResponseCode();
-        if (! postRC.equals(200)) {
-            log.warn(post.getErrorStream().getText());
-        }
-    }
-
-    //
-    // Dump pipeline parameters in a json file
-    //
-    public static void dump_parameters(workflow, params) {
-        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-        def filename   = "params_${timestamp}.json"
-        def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-        def jsonStr    = JsonOutput.toJson(params)
-        temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
-
-        FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
-        temp_pf.delete()
-    }
-
-    //
-    // Print pipeline summary on completion
-    //
-    public static void summary(workflow, params, log, pass_mapped_reads=[:], pass_trimmed_reads=[:], pass_strand_check=[:]) {
-        Map colors = logColours(params.monochrome_logs)
-
-        def fail_mapped_count  = pass_mapped_reads.count  { key, value -> value == false }
-        def fail_trimmed_count = pass_trimmed_reads.count { key, value -> value == false }
-        def fail_strand_count  = pass_strand_check.count  { key, value -> value == false }
-        if (workflow.success) {
-            def color = colors.green
-            def status = []
-            if (workflow.stats.ignoredCount != 0) {
-                color = colors.yellow
-                status += ['with errored process(es)']
-            }
-            if (fail_mapped_count > 0 || fail_trimmed_count > 0 || fail_strand_count > 0) {
-                color = colors.yellow
-                status += ['with skipped sampl(es)']
-            }
-            log.info "-${colors.purple}[$workflow.manifest.name]${color} Pipeline completed successfully ${status.join(', ')}${colors.reset}-"
-            if (fail_trimmed_count > 0) {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_trimmed_count}/${pass_trimmed_reads.size()} samples skipped since they failed ${params.min_trimmed_reads} trimmed read threshold.${colors.reset}-"
-            }
-            if (fail_mapped_count > 0) {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_mapped_count}/${pass_mapped_reads.size()} samples skipped since they failed STAR ${params.min_mapped_reads}% mapped threshold.${colors.reset}-"
-            }
-            if (fail_strand_count > 0) {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_strand_count}/${pass_strand_check.size()} samples failed strandedness check.${colors.reset}-"
-            }
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
-        }
-    }
-
-    //
-    // ANSII Colours used for terminal logging
-    //
-    public static Map logColours(Boolean monochrome_logs) {
-        Map colorcodes = [:]
-
-        // Reset / Meta
-        colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
-        colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
-        colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
-        colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
-        colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
-        colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
-        colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
-
-        // Regular Colors
-        colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-        colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-        colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-        colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-        colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-        colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-        colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-        colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
-
-        // Bold
-        colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-        colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-        colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-        colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-        colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-        colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-        colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-        colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
-
-        // Underline
-        colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-        colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-        colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-        colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-        colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-        colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-        colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-        colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
-
-        // High Intensity
-        colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-        colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-        colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-        colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-        colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-        colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-        colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-        colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
-
-        // Bold High Intensity
-        colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-        colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-        colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-        colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-        colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-        colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-        colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-        colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
-
-        return colorcodes
-    }
-
-    //
-    // Does what is says on the tin
-    //
-    public static String dashedLine(monochrome_logs) {
-        Map colors = logColours(monochrome_logs)
-        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-    }
-
-    //
-    // nf-core logo
-    //
-    public static String logo(workflow, monochrome_logs) {
-        Map colors = logColours(monochrome_logs)
-        String workflow_version = NfcoreTemplate.version(workflow)
-        String.format(
-            """\n
-            ${dashedLine(monochrome_logs)}
-                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                    ${colors.green}`._,._,\'${colors.reset}
-            ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
-            ${dashedLine(monochrome_logs)}
-            """.stripIndent()
-        )
-    }
-}
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
deleted file mode 100644
index 8d030f4e8..000000000
--- a/lib/Utils.groovy
+++ /dev/null
@@ -1,47 +0,0 @@
-//
-// This file holds several Groovy functions that could be useful for any Nextflow pipeline
-//
-
-import org.yaml.snakeyaml.Yaml
-
-class Utils {
-
-    //
-    // When running with -profile conda, warn if channels have not been set-up appropriately
-    //
-    public static void checkCondaChannels(log) {
-        Yaml parser = new Yaml()
-        def channels = []
-        try {
-            def config = parser.load("conda config --show channels".execute().text)
-            channels = config.channels
-        } catch(NullPointerException | IOException e) {
-            log.warn "Could not verify conda channel configuration."
-            return
-        }
-
-        // Check that all channels are present
-        // This channel list is ordered by required channel priority.
-        def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
-        def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
-
-        // Check that they are in the right order
-        def channel_priority_violation = false
-        def n = required_channels_in_order.size()
-        for (int i = 0; i < n - 1; i++) {
-            channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
-        }
-
-        if (channels_missing | channel_priority_violation) {
-            log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                "  There is a problem with your Conda configuration!\n\n" +
-                "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-                "  Please refer to https://bioconda.github.io/\n" +
-                "  The observed channel order is \n" +
-                "  ${channels}\n" +
-                "  but the following channel order is required:\n" +
-                "  ${required_channels_in_order}\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        }
-    }
-}
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
deleted file mode 100755
index 4d94dfe08..000000000
--- a/lib/WorkflowMain.groovy
+++ /dev/null
@@ -1,60 +0,0 @@
-//
-// This file holds several functions specific to the main.nf workflow in the nf-core/rnaseq pipeline
-//
-
-import nextflow.Nextflow
-
-class WorkflowMain {
-
-    //
-    // Citation string for pipeline
-    //
-    public static String citation(workflow) {
-        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            "* The pipeline\n" +
-            "  https://doi.org/10.5281/zenodo.1400710\n\n" +
-            "* The nf-core framework\n" +
-            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-            "* Software dependencies\n" +
-            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-    }
-
-    //
-    // Validate parameters and print summary to screen
-    //
-    public static void initialise(workflow, params, log) {
-
-        // Print workflow version and exit on --version
-        if (params.version) {
-            String workflow_version = NfcoreTemplate.version(workflow)
-            log.info "${workflow.manifest.name} ${workflow_version}"
-            System.exit(0)
-        }
-
-        // Warn about using custom configs to provide pipeline parameters
-        NfcoreTemplate.warnParamsProvidedInConfig(workflow, log)
-
-        // Check that a -profile or Nextflow config has been provided to run the pipeline
-        NfcoreTemplate.checkConfigProvided(workflow, log)
-
-        // Check that conda channels are set-up correctly
-        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-            Utils.checkCondaChannels(log)
-        }
-
-        // Check AWS batch settings
-        NfcoreTemplate.awsBatch(workflow, params)
-    }
-
-    //
-    // Get attribute from genome config file e.g. fasta
-    //
-    public static Object getGenomeAttribute(params, attribute) {
-        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-            if (params.genomes[ params.genome ].containsKey(attribute)) {
-                return params.genomes[ params.genome ][ attribute ]
-            }
-        }
-        return null
-    }
-}
diff --git a/lib/WorkflowRnaseq.groovy b/lib/WorkflowRnaseq.groovy
deleted file mode 100755
index 29a1724e3..000000000
--- a/lib/WorkflowRnaseq.groovy
+++ /dev/null
@@ -1,474 +0,0 @@
-//
-// This file holds several functions specific to the workflow/rnaseq.nf in the nf-core/rnaseq pipeline
-//
-
-import nextflow.Nextflow
-import groovy.json.JsonSlurper
-import groovy.text.SimpleTemplateEngine
-
-class WorkflowRnaseq {
-
-    //
-    // Check and validate parameters
-    //
-    public static void initialise(params, log) {
-        genomeExistsError(params, log)
-
-        if (!params.fasta) {
-            Nextflow.error("Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.")
-        }
-
-        if (!params.gtf && !params.gff) {
-            Nextflow.error("No GTF or GFF3 annotation specified! The pipeline requires at least one of these files.")
-        }
-
-        if (params.gtf) {
-            if (params.gff) {
-                gtfGffWarn(log)
-            }
-            if (params.genome == 'GRCh38' && params.gtf.contains('Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf')) {
-                ncbiGenomeWarn(log)
-            }
-            if (params.gtf.contains('/UCSC/') && params.gtf.contains('Annotation/Genes/genes.gtf')) {
-                ucscGenomeWarn(log)
-            }
-        }
-
-        if (params.transcript_fasta) {
-            transcriptsFastaWarn(log)
-        }
-
-        if (!params.skip_bbsplit && !params.bbsplit_index && !params.bbsplit_fasta_list) {
-            Nextflow.error("Please provide either --bbsplit_fasta_list / --bbsplit_index to run BBSplit.")
-        }
-
-        if (params.remove_ribo_rna && !params.ribo_database_manifest) {
-            Nextflow.error("Please provide --ribo_database_manifest to remove ribosomal RNA with SortMeRNA.")
-        }
-
-
-        if (params.with_umi && !params.skip_umi_extract) {
-            if (!params.umitools_bc_pattern && !params.umitools_bc_pattern2) {
-                Nextflow.error("UMI-tools requires a barcode pattern to extract barcodes from the reads.")
-            }
-        }
-
-        if (params.skip_alignment) {
-            skipAlignmentWarn(log)
-        }
-
-        if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
-            if (!(params.salmon_index || params.transcript_fasta || (params.fasta && (params.gtf || params.gff)))) {
-                Nextflow.error("To use `--pseudo_aligner 'salmon'`, you must provide either --salmon_index or --transcript_fasta or both --fasta and --gtf / --gff.")
-            }
-        }
-
-        // Checks when running --aligner star_rsem
-        if (!params.skip_alignment && params.aligner == 'star_rsem') {
-            if (params.with_umi) {
-                rsemUmiError(log)
-            }
-            if (params.rsem_index && params.star_index) {
-                rsemStarIndexWarn(log)
-            }
-            if (params.aligner  == 'star_rsem' && params.extra_star_align_args) {
-                rsemStarExtraArgumentsWarn(log)
-            }
-        }
-
-        // Warn if --additional_fasta provided with aligner index
-        if (!params.skip_alignment && params.additional_fasta) {
-            def index = ''
-            if (params.aligner == 'star_salmon' && params.star_index) {
-                index = 'star'
-            }
-            if (params.aligner == 'star_rsem' && params.rsem_index) {
-                index = 'rsem'
-            }
-            if (params.aligner == 'hisat2' && params.hisat2_index) {
-                index = 'hisat2'
-            }
-            if (index) {
-                additionaFastaIndexWarn(index, log)
-            }
-        }
-
-        // Check which RSeQC modules we are running
-        def valid_rseqc_modules = ['bam_stat', 'inner_distance', 'infer_experiment', 'junction_annotation', 'junction_saturation', 'read_distribution', 'read_duplication', 'tin']
-        def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
-        if ((valid_rseqc_modules + rseqc_modules).unique().size() != valid_rseqc_modules.size()) {
-            Nextflow.error("Invalid option: ${params.rseqc_modules}. Valid options for '--rseqc_modules': ${valid_rseqc_modules.join(', ')}")
-        }
-    }
-
-    //
-    // Function to validate channels from input samplesheet
-    //
-    public static ArrayList validateInput(input) {
-        def (metas, fastqs) = input[1..2]
-
-        // Check that multiple runs of the same sample are of the same strandedness
-        def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1
-        if (!strandedness_ok) {
-            Nextflow.error("Please check input samplesheet -> Multiple runs of a sample must have the same strandedness!: ${metas[0].id}")
-        }
-
-        // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-        def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
-        if (!endedness_ok) {
-            Nextflow.error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
-        }
-
-        return [ metas[0], fastqs ]
-    }
-
-    //
-    // Function to check whether biotype field exists in GTF file
-    //
-    public static Boolean biotypeInGtf(gtf_file, biotype, log) {
-        def hits = 0
-        gtf_file.eachLine { line ->
-            def attributes = line.split('\t')[-1].split()
-            if (attributes.contains(biotype)) {
-                hits += 1
-            }
-        }
-        if (hits) {
-            return true
-        } else {
-            log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                "  Biotype attribute '${biotype}' not found in the last column of the GTF file!\n\n" +
-                "  Biotype QC will be skipped to circumvent the issue below:\n" +
-                "  https://github.com/nf-core/rnaseq/issues/460\n\n" +
-                "  Amend '--featurecounts_group_type' to change this behaviour.\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-            return false
-        }
-    }
-
-    //
-    // Function to generate an error if contigs in genome fasta file > 512 Mbp
-    //
-    public static void checkMaxContigSize(fai_file, log) {
-        def max_size = 512000000
-        fai_file.eachLine { line ->
-            def lspl  = line.split('\t')
-            def chrom = lspl[0]
-            def size  = lspl[1]
-            if (size.toInteger() > max_size) {
-                def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                    "  Contig longer than ${max_size}bp found in reference genome!\n\n" +
-                    "  ${chrom}: ${size}\n\n" +
-                    "  Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.\n\n" +
-                    "  Please see:\n" +
-                    "  https://github.com/nf-core/rnaseq/issues/744\n" +
-                    "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-                Nextflow.error(error_string)
-            }
-        }
-    }
-
-    //
-    // Function that parses Salmon quant 'meta_info.json' output file to get inferred strandedness
-    //
-    public static String getSalmonInferredStrandedness(json_file) {
-        def lib_type = new JsonSlurper().parseText(json_file.text).get('library_types')[0]
-        def strandedness = 'reverse'
-        if (lib_type) {
-            if (lib_type in ['U', 'IU']) {
-                strandedness = 'unstranded'
-            } else if (lib_type in ['SF', 'ISF']) {
-                strandedness = 'forward'
-            } else if (lib_type in ['SR', 'ISR']) {
-                strandedness = 'reverse'
-            }
-        }
-        return strandedness
-    }
-
-    //
-    // Function that parses TrimGalore log output file to get total number of reads after trimming
-    //
-    public static Integer getTrimGaloreReadsAfterFiltering(log_file) {
-        def total_reads = 0
-        def filtered_reads = 0
-        log_file.eachLine { line ->
-            def total_reads_matcher = line =~ /([\d\.]+)\ssequences processed in total/
-            def filtered_reads_matcher = line =~ /shorter than the length cutoff[^:]+:\s([\d\.]+)/
-            if (total_reads_matcher) total_reads = total_reads_matcher[0][1].toFloat()
-            if (filtered_reads_matcher) filtered_reads = filtered_reads_matcher[0][1].toFloat()
-        }
-        return total_reads - filtered_reads
-    }
-
-    //
-    // Function that parses and returns the alignment rate from the STAR log output
-    //
-    public static ArrayList getStarPercentMapped(params, align_log) {
-        def percent_aligned = 0
-        def pattern = /Uniquely mapped reads %\s*\|\s*([\d\.]+)%/
-        align_log.eachLine { line ->
-            def matcher = line =~ pattern
-            if (matcher) {
-                percent_aligned = matcher[0][1].toFloat()
-            }
-        }
-
-        def pass = false
-        if (percent_aligned >= params.min_mapped_reads.toFloat()) {
-            pass = true
-        }
-        return [ percent_aligned, pass ]
-    }
-
-    //
-    // Function that parses and returns the predicted strandedness from the RSeQC infer_experiment.py output
-    //
-    public static ArrayList getInferexperimentStrandedness(inferexperiment_file, cutoff=30) {
-        def sense        = 0
-        def antisense    = 0
-        def undetermined = 0
-        inferexperiment_file.eachLine { line ->
-            def undetermined_matcher = line =~ /Fraction of reads failed to determine:\s([\d\.]+)/
-            def se_sense_matcher     = line =~ /Fraction of reads explained by "\++,--":\s([\d\.]+)/
-            def se_antisense_matcher = line =~ /Fraction of reads explained by "\+-,-\+":\s([\d\.]+)/
-            def pe_sense_matcher     = line =~ /Fraction of reads explained by "1\++,1--,2\+-,2-\+":\s([\d\.]+)/
-            def pe_antisense_matcher = line =~ /Fraction of reads explained by "1\+-,1-\+,2\+\+,2--":\s([\d\.]+)/
-            if (undetermined_matcher) undetermined = undetermined_matcher[0][1].toFloat() * 100
-            if (se_sense_matcher)     sense        = se_sense_matcher[0][1].toFloat() * 100
-            if (se_antisense_matcher) antisense    = se_antisense_matcher[0][1].toFloat() * 100
-            if (pe_sense_matcher)     sense        = pe_sense_matcher[0][1].toFloat() * 100
-            if (pe_antisense_matcher) antisense    = pe_antisense_matcher[0][1].toFloat() * 100
-        }
-        def strandedness = 'unstranded'
-        if (sense >= 100-cutoff) {
-            strandedness = 'forward'
-        } else if (antisense >= 100-cutoff) {
-            strandedness = 'reverse'
-        }
-        return [ strandedness, sense, antisense, undetermined ]
-    }
-
-    //
-    // Get workflow summary for MultiQC
-    //
-    public static String paramsSummaryMultiqc(workflow, summary) {
-        String summary_section = ''
-        for (group in summary.keySet()) {
-            def group_params = summary.get(group)  // This gets the parameters of that particular group
-            if (group_params) {
-                summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
-                summary_section += "    <dl class=\"dl-horizontal\">\n"
-                for (param in group_params.keySet()) {
-                    summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
-                }
-                summary_section += "    </dl>\n"
-            }
-        }
-
-        String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
-        yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
-        yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-        yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-        yaml_file_text        += "plot_type: 'html'\n"
-        yaml_file_text        += "data: |\n"
-        yaml_file_text        += "${summary_section}"
-        return yaml_file_text
-    }
-
-    //
-    // Generate methods description for MultiQC
-    //
-    public static String toolCitationText(params) {
-        // TODO nf-core: Optionally add in-text citation tools to this list.
-        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
-        // Uncomment function in methodsDescriptionText to render in MultiQC report
-        def citation_text = [
-                "Tools used in the workflow included:",
-                "FastQC (Andrews 2010),",
-                "MultiQC (Ewels et al. 2016)",
-                "."
-            ].join(' ').trim()
-
-        return citation_text
-    }
-
-    public static String toolBibliographyText(params) {
-        // TODO Optionally add bibliographic entries to this list.
-        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
-        // Uncomment function in methodsDescriptionText to render in MultiQC report
-        def reference_text = [
-                "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
-                "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
-            ].join(' ').trim()
-
-        return reference_text
-    }
-
-    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) {
-        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
-        def meta = [:]
-        meta.workflow = run_workflow.toMap()
-        meta["manifest_map"] = run_workflow.manifest.toMap()
-
-        // Pipeline DOI
-        meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
-        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
-
-        // Tool references
-        meta["tool_citations"] = ""
-        meta["tool_bibliography"] = ""
-
-        // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
-        //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-        //meta["tool_bibliography"] = toolBibliographyText(params)
-
-        def methods_text = mqc_methods_yaml.text
-
-        def engine =  new SimpleTemplateEngine()
-        def description_html = engine.createTemplate(methods_text).make(meta)
-
-        return description_html
-    }
-
-    //
-    // Create MultiQC tsv custom content from a list of values
-    //
-    public static String multiqcTsvFromList(tsv_data, header) {
-        def tsv_string = ""
-        if (tsv_data.size() > 0) {
-            tsv_string += "${header.join('\t')}\n"
-            tsv_string += tsv_data.join('\n')
-        }
-        return tsv_string
-    }
-
-    //
-    // Exit pipeline if incorrect --genome key provided
-    //
-    private static void genomeExistsError(params, log) {
-        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-            def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-                "  Currently, the available genome keys are:\n" +
-                "  ${params.genomes.keySet().join(", ")}\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-            Nextflow.error(error_string)
-        }
-    }
-
-    //
-    // Print a warning if using GRCh38 assembly from igenomes.config
-    //
-    private static void ncbiGenomeWarn(log) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  When using '--genome GRCh38' the assembly is from the NCBI and NOT Ensembl.\n" +
-            "  Biotype QC will be skipped to circumvent the issue below:\n" +
-            "  https://github.com/nf-core/rnaseq/issues/460\n\n" +
-            "  If you would like to use the soft-masked Ensembl assembly instead please see:\n" +
-            "  https://github.com/nf-core/rnaseq/issues/159#issuecomment-501184312\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-    }
-
-    //
-    // Print a warning if using a UCSC assembly from igenomes.config
-    //
-    private static void ucscGenomeWarn(log) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  When using UCSC assemblies the 'gene_biotype' field is absent from the GTF file.\n" +
-            "  Biotype QC will be skipped to circumvent the issue below:\n" +
-            "  https://github.com/nf-core/rnaseq/issues/460\n\n" +
-            "  If you would like to use the soft-masked Ensembl assembly instead please see:\n" +
-            "  https://github.com/nf-core/rnaseq/issues/159#issuecomment-501184312\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-    }
-
-    //
-    // Print a warning if both GTF and GFF have been provided
-    //
-    private static void gtfGffWarn(log) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  Both '--gtf' and '--gff' parameters have been provided.\n" +
-            "  Using GTF file as priority.\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-    }
-
-    //
-    // Print a warning if using '--transcript_fasta'
-    //
-    private static void transcriptsFastaWarn(log) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  '--transcript_fasta' parameter has been provided.\n" +
-            "  Make sure transcript names in this file match those in the GFF/GTF file.\n\n" +
-            "  Please see:\n" +
-            "  https://github.com/nf-core/rnaseq/issues/753\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-    }
-
-    //
-    // Print a warning if --skip_alignment has been provided
-    //
-    private static void skipAlignmentWarn(log) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  '--skip_alignment' parameter has been provided.\n" +
-            "  Skipping alignment, genome-based quantification and all downstream QC processes.\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-    }
-
-    //
-    // Print a warning if using '--aligner star_rsem' and '--with_umi'
-    //
-    private static void rsemUmiError(log) {
-        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  When using '--aligner star_rsem', STAR is run by RSEM itself and so it is\n" +
-            "  not possible to remove UMIs before the quantification.\n\n" +
-            "  If you would like to remove UMI barcodes using the '--with_umi' option\n" +
-            "  please use either '--aligner star_salmon' or '--aligner hisat2'.\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        Nextflow.error(error_string)
-    }
-
-    //
-    // Print a warning if using '--aligner star_rsem' and providing both '--rsem_index' and '--star_index'
-    //
-    private static void rsemStarIndexWarn(log) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  When using '--aligner star_rsem', both the STAR and RSEM indices should\n" +
-            "  be present in the path specified by '--rsem_index'.\n\n" +
-            "  This warning has been generated because you have provided both\n" +
-            "  '--rsem_index' and '--star_index'. The pipeline will ignore the latter.\n\n" +
-            "  Please see:\n" +
-            "  https://github.com/nf-core/rnaseq/issues/568\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-    }
-
-    //
-    // Print a warning if using '--aligner star_rsem' and providing '--star_extra_alignment_args'
-    //
-    private static void rsemStarExtraArgumentsWarn(log) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  No additional arguments can be passed to STAR when using RSEM.\n" +
-            "  Because RSEM enforces its own parameters for STAR, any extra arguments\n" +
-            "  to STAR will be ignored. Alternatively, choose the STAR+Salmon route.\n\n" +
-            "  This warning has been generated because you have provided both\n" +
-            "  '--aligner star_rsem' and '--extra_star_align_args'.\n\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-    }
-
-    //
-    // Print a warning if using '--additional_fasta' and '--<ALIGNER>_index'
-    //
-    private static void additionaFastaIndexWarn(index, log) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  When using '--additional_fasta <FASTA_FILE>' the aligner index will not\n" +
-            "  be re-built with the transgenes incorporated by default since you have \n" +
-            "  already provided an index via '--${index}_index <INDEX>'.\n\n" +
-            "  Set '--additional_fasta <FASTA_FILE> --${index}_index false --gene_bed false --save_reference'\n" +
-            "  to re-build the index with transgenes included and the index and gene BED file will be saved in\n" +
-            "  'results/genome/index/${index}/' for re-use with '--${index}_index'.\n\n" +
-            "  Ignore this warning if you know that the index already contains transgenes.\n\n" +
-            "  Please see:\n" +
-            "  https://github.com/nf-core/rnaseq/issues/556\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-    }
-}
diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar
deleted file mode 100644
index 805c8bb5e..000000000
Binary files a/lib/nfcore_external_java_deps.jar and /dev/null differ
diff --git a/main.nf b/main.nf
index 69ae6c3b3..a0a6f1c7d 100755
--- a/main.nf
+++ b/main.nf
@@ -17,70 +17,184 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.fasta            = WorkflowMain.getGenomeAttribute(params, 'fasta')
-params.transcript_fasta = WorkflowMain.getGenomeAttribute(params, 'transcript_fasta')
-params.additional_fasta = WorkflowMain.getGenomeAttribute(params, 'additional_fasta')
-params.gtf              = WorkflowMain.getGenomeAttribute(params, 'gtf')
-params.gff              = WorkflowMain.getGenomeAttribute(params, 'gff')
-params.gene_bed         = WorkflowMain.getGenomeAttribute(params, 'bed12')
-params.bbsplit_index    = WorkflowMain.getGenomeAttribute(params, 'bbsplit')
-params.star_index       = WorkflowMain.getGenomeAttribute(params, 'star')
-params.hisat2_index     = WorkflowMain.getGenomeAttribute(params, 'hisat2')
-params.rsem_index       = WorkflowMain.getGenomeAttribute(params, 'rsem')
-params.salmon_index     = WorkflowMain.getGenomeAttribute(params, 'salmon')
-params.kallisto_index   = WorkflowMain.getGenomeAttribute(params, 'kallisto')
+params.fasta            = getGenomeAttribute('fasta')
+params.additional_fasta = getGenomeAttribute('additional_fasta')
+params.transcript_fasta = getGenomeAttribute('transcript_fasta')
+params.gff              = getGenomeAttribute('gff')
+params.gtf              = getGenomeAttribute('gtf')
+params.gene_bed         = getGenomeAttribute('bed12')
+params.bbsplit_index    = getGenomeAttribute('bbsplit')
+params.sortmerna_index  = getGenomeAttribute('sortmerna')
+params.star_index       = getGenomeAttribute('star')
+params.rsem_index       = getGenomeAttribute('rsem')
+params.hisat2_index     = getGenomeAttribute('hisat2')
+params.salmon_index     = getGenomeAttribute('salmon')
+params.kallisto_index   = getGenomeAttribute('kallisto')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    VALIDATE & PRINT PARAMETER SUMMARY
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
+include { RNASEQ                  } from './workflows/rnaseq'
+include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { checkMaxContigSize      } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
 
-// Print help message if needed
-if (params.help) {
-    def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
-    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
-    System.exit(0)
-}
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    NAMED WORKFLOWS FOR PIPELINE
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
 
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
+//
+// WORKFLOW: Run main analysis pipeline
+//
+workflow NFCORE_RNASEQ {
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    //
+    // SUBWORKFLOW: Prepare reference genome files
+    //
+    PREPARE_GENOME (
+        params.fasta,
+        params.gtf,
+        params.gff,
+        params.additional_fasta,
+        params.transcript_fasta,
+        params.gene_bed,
+        params.splicesites,
+        params.bbsplit_fasta_list,
+        params.ribo_database_manifest,
+        params.star_index,
+        params.rsem_index,
+        params.salmon_index,
+        params.kallisto_index,
+        params.hisat2_index,
+        params.bbsplit_index,
+        params.sortmerna_index,
+        params.gencode,
+        params.featurecounts_group_type,
+        params.aligner,
+        params.pseudo_aligner,
+        params.skip_gtf_filter,
+        params.skip_bbsplit,
+        !params.remove_ribo_rna,
+        params.skip_alignment,
+        params.skip_pseudo_alignment
+    )
+    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
+
+    // Check if contigs in genome fasta file > 512 Mbp
+    if (!params.skip_alignment && !params.bam_csi_index) {
+        PREPARE_GENOME
+            .out
+            .fai
+            .map { checkMaxContigSize(it) }
+    }
 
-WorkflowMain.initialise(workflow, params, log)
+    //
+    // WORKFLOW: Run nf-core/rnaseq workflow
+    //
+    ch_samplesheet = Channel.value(file(params.input, checkIfExists: true))
+    RNASEQ (
+        ch_samplesheet,
+        ch_versions,
+        PREPARE_GENOME.out.fasta,
+        PREPARE_GENOME.out.gtf,
+        PREPARE_GENOME.out.fai,
+        PREPARE_GENOME.out.chrom_sizes,
+        PREPARE_GENOME.out.gene_bed,
+        PREPARE_GENOME.out.transcript_fasta,
+        PREPARE_GENOME.out.star_index,
+        PREPARE_GENOME.out.rsem_index,
+        PREPARE_GENOME.out.hisat2_index,
+        PREPARE_GENOME.out.salmon_index,
+        PREPARE_GENOME.out.kallisto_index,
+        PREPARE_GENOME.out.bbsplit_index,
+        PREPARE_GENOME.out.rrna_fastas,
+        PREPARE_GENOME.out.sortmerna_index,
+        PREPARE_GENOME.out.splicesites,
+        !params.remove_ribo_rna && params.remove_ribo_rna
+    )
+    ch_versions = ch_versions.mix(RNASEQ.out.versions)
+
+    emit:
+    trim_status    = RNASEQ.out.trim_status    // channel: [id, boolean]
+    map_status     = RNASEQ.out.map_status     // channel: [id, boolean]
+    strand_status  = RNASEQ.out.strand_status  // channel: [id, boolean]
+    multiqc_report = RNASEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
+    versions       = ch_versions               // channel: [version1, version2, ...]
+}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOW FOR PIPELINE
+    RUN MAIN WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { RNASEQ } from './workflows/rnaseq'
+workflow {
 
-//
-// WORKFLOW: Run main nf-core/rnaseq analysis pipeline
-//
-workflow NFCORE_RNASEQ {
-    RNASEQ ()
+    main:
+
+    //
+    // SUBWORKFLOW: Run initialisation tasks
+    //
+    PIPELINE_INITIALISATION (
+        params.version,
+        params.help,
+        "nextflow_schema.json",
+        params.validate_params,
+        params.monochrome_logs,
+        args,
+        params.outdir
+    )
+
+    //
+    // WORKFLOW: Run main workflow
+    //
+    NFCORE_RNASEQ ()
+
+    //
+    // SUBWORKFLOW: Run completion tasks
+    //
+    PIPELINE_COMPLETION (
+        "nextflow_schema.json",
+        params.email,
+        params.email_on_fail,
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url,
+        NFCORE_RNASEQ.out.multiqc_report,
+        NFCORE_RNASEQ.out.trim_status,
+        NFCORE_RNASEQ.out.map_status,
+        NFCORE_RNASEQ.out.strand_status
+    )
 }
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN ALL WORKFLOWS
+    FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
-// WORKFLOW: Execute a single named workflow for the pipeline
-// See: https://github.com/nf-core/rnaseq/issues/619
+// Get attribute from genome config file e.g. fasta
 //
-workflow {
-    NFCORE_RNASEQ ()
+
+def getGenomeAttribute(attribute) {
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[ params.genome ].containsKey(attribute)) {
+            return params.genomes[ params.genome ][ attribute ]
+        }
+    }
+    return null
 }
 
 /*
diff --git a/modules.json b/modules.json
index 113f5139f..6e266bc86 100644
--- a/modules.json
+++ b/modules.json
@@ -7,245 +7,267 @@
                 "nf-core": {
                     "bbmap/bbsplit": {
                         "branch": "master",
-                        "git_sha": "de3e6fc949dcffb8d3508c015f435ace5773ff08",
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
+                    },
+                    "bedtools/genomecov": {
+                        "branch": "master",
+                        "git_sha": "9ba6b02bbcb322ff4265cc51fca0ee5d8420b929",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
-                        "installed_by": ["modules"]
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
                     },
-                    "custom/dumpsoftwareversions": {
+                    "custom/catadditionalfasta": {
                         "branch": "master",
-                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "installed_by": ["modules"]
                     },
                     "custom/getchromsizes": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "installed_by": ["modules"]
+                    },
+                    "custom/tx2gene": {
+                        "branch": "master",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "installed_by": ["modules", "quantify_pseudo_alignment"]
+                    },
+                    "dupradar": {
+                        "branch": "master",
+                        "git_sha": "055416736dcb4955960ecc17dea61eb41b68c024",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"],
-                        "patch": "modules/nf-core/fastp/fastp.diff"
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a",
-                        "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"],
-                        "patch": "modules/nf-core/fastqc/fastqc.diff"
+                        "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5",
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "fq/subsample": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules", "fastq_subsample_fq_salmon"]
+                        "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
+                        "installed_by": ["fastq_subsample_fq_salmon", "modules"]
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
+                        "git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "hisat2/align": {
                         "branch": "master",
-                        "git_sha": "a1881f6374506f9e031b7af814768cdb44a6a7d3",
+                        "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "hisat2/build": {
                         "branch": "master",
-                        "git_sha": "f2f48836bf5c59434966a6c3b2211b29363f31ab",
+                        "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
                         "installed_by": ["modules"]
                     },
                     "hisat2/extractsplicesites": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
                         "installed_by": ["modules"]
                     },
                     "kallisto/index": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
                         "installed_by": ["modules"]
                     },
                     "kallisto/quant": {
                         "branch": "master",
-                        "git_sha": "bdc2a97ced7adc423acfa390742db83cab98c1ad",
+                        "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
+                        "installed_by": ["modules", "quantify_pseudo_alignment"]
+                    },
+                    "multiqc": {
+                        "branch": "master",
+                        "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
-                        "installed_by": ["bam_markduplicates_picard"]
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "installed_by": ["bam_markduplicates_picard"],
+                        "patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff"
                     },
                     "preseq/lcextrap": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
                         "installed_by": ["modules"]
                     },
                     "qualimap/rnaseq": {
                         "branch": "master",
-                        "git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff"
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "installed_by": ["modules"]
                     },
                     "rsem/calculateexpression": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
                         "installed_by": ["modules"]
                     },
                     "rsem/preparereference": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
                         "installed_by": ["modules"]
                     },
                     "rseqc/bamstat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"],
-                        "patch": "modules/nf-core/rseqc/bamstat/rseqc-bamstat.diff"
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/inferexperiment": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"],
-                        "patch": "modules/nf-core/rseqc/inferexperiment/rseqc-inferexperiment.diff"
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/innerdistance": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"],
-                        "patch": "modules/nf-core/rseqc/innerdistance/rseqc-innerdistance.diff"
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/junctionannotation": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"],
-                        "patch": "modules/nf-core/rseqc/junctionannotation/rseqc-junctionannotation.diff"
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/junctionsaturation": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"],
-                        "patch": "modules/nf-core/rseqc/junctionsaturation/rseqc-junctionsaturation.diff"
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/readdistribution": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"],
-                        "patch": "modules/nf-core/rseqc/readdistribution/rseqc-readdistribution.diff"
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/readduplication": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"],
-                        "patch": "modules/nf-core/rseqc/readduplication/rseqc-readduplication.diff"
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/tin": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"],
-                        "patch": "modules/nf-core/rseqc/tin/rseqc-tin.diff"
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["bam_rseqc"]
                     },
                     "salmon/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cb6b2b94fc40dea58f0b1e3dd095f3dd24f2ac8a",
                         "installed_by": ["fastq_subsample_fq_salmon"]
                     },
                     "salmon/quant": {
                         "branch": "master",
-                        "git_sha": "c5b528d0a51c31621b485ab3bcc008f483619ea6",
-                        "installed_by": ["modules", "fastq_subsample_fq_salmon"]
+                        "git_sha": "727232afb8294b53dd9d05bfe469b70cce1675bb",
+                        "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": [
+                            "bam_dedup_stats_samtools_umitools",
                             "bam_markduplicates_picard",
-                            "bam_sort_stats_samtools",
-                            "bam_dedup_stats_samtools_umitools"
+                            "bam_sort_stats_samtools"
                         ]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "sortmerna": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "df05c8db5195867c0bc7b92c1788115b66f0d17d",
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "stringtie/stringtie": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b",
                         "installed_by": ["modules"]
                     },
                     "subread/featurecounts": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
                         "installed_by": ["modules"]
                     },
+                    "summarizedexperiment/summarizedexperiment": {
+                        "branch": "master",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "installed_by": ["modules", "quantify_pseudo_alignment"]
+                    },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore"]
                     },
+                    "tximeta/tximport": {
+                        "branch": "master",
+                        "git_sha": "d612c281cf2fae62cdd79c70a22fc6349108570c",
+                        "installed_by": ["modules", "quantify_pseudo_alignment"]
+                    },
                     "ucsc/bedclip": {
                         "branch": "master",
-                        "git_sha": "240937a2a9c30298110753292be041188891f2cb",
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
                         "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
                     "ucsc/bedgraphtobigwig": {
                         "branch": "master",
-                        "git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
                     "umitools/dedup": {
                         "branch": "master",
-                        "git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
-                        "installed_by": ["bam_dedup_stats_samtools_umitools"],
-                        "patch": "modules/nf-core/umitools/dedup/umitools-dedup.diff"
+                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
+                        "installed_by": ["bam_dedup_stats_samtools_umitools"]
                     },
                     "umitools/extract": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"],
-                        "patch": "modules/nf-core/umitools/extract/umitools-extract.diff"
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
+                    },
+                    "umitools/prepareforrsem": {
+                        "branch": "master",
+                        "git_sha": "fac6cc9b2bc4042225bd9247ec03b413f764b47f",
+                        "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     }
                 }
@@ -254,56 +276,81 @@
                 "nf-core": {
                     "bam_dedup_stats_samtools_umitools": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_rseqc": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
                         "installed_by": [
-                            "bam_sort_stats_samtools",
+                            "bam_dedup_stats_samtools_umitools",
                             "bam_markduplicates_picard",
-                            "bam_dedup_stats_samtools_umitools"
+                            "bam_sort_stats_samtools"
                         ]
                     },
                     "bedgraph_bedclip_bedgraphtobigwig": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_hisat2": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_fastqc_umitools_fastp": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
-                        "installed_by": ["subworkflows"]
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
                     },
                     "fastq_fastqc_umitools_trimgalore": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5",
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
+                    },
+                    "fastq_qc_trim_filter_setstrandedness": {
+                        "branch": "master",
+                        "git_sha": "8c47be6a114b82a6e6d2f5320b3b5c67579956c0",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_subsample_fq_salmon": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
+                    },
+                    "quantify_pseudo_alignment": {
+                        "branch": "master",
+                        "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "utils_nextflow_pipeline": {
+                        "branch": "master",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "utils_nfcore_pipeline": {
+                        "branch": "master",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "utils_nfvalidation_plugin": {
+                        "branch": "master",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/local/bedtools_genomecov/main.nf b/modules/local/bedtools_genomecov/main.nf
deleted file mode 100644
index 0a0fb3c8b..000000000
--- a/modules/local/bedtools_genomecov/main.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-process BEDTOOLS_GENOMECOV {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "bioconda::bedtools=2.30.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-        'biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-
-    input:
-    tuple val(meta), path(bam)
-
-    output:
-    tuple val(meta), path("*.forward.bedGraph"), emit: bedgraph_forward
-    tuple val(meta), path("*.reverse.bedGraph"), emit: bedgraph_reverse
-    path "versions.yml"                        , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    def prefix_forward = "${prefix}.forward"
-    def prefix_reverse = "${prefix}.reverse"
-    if (meta.strandedness == 'reverse') {
-        prefix_forward = "${prefix}.reverse"
-        prefix_reverse = "${prefix}.forward"
-    }
-    """
-    bedtools \\
-        genomecov \\
-        -ibam $bam \\
-        -bg \\
-        -strand + \\
-        $args \\
-        | bedtools sort > ${prefix_forward}.bedGraph
-
-    bedtools \\
-        genomecov \\
-        -ibam $bam \\
-        -bg \\
-        -strand - \\
-        $args \\
-        | bedtools sort > ${prefix_reverse}.bedGraph
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/cat_additional_fasta/main.nf b/modules/local/cat_additional_fasta/main.nf
deleted file mode 100644
index 72af4bc54..000000000
--- a/modules/local/cat_additional_fasta/main.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-process CAT_ADDITIONAL_FASTA {
-    tag "$add_fasta"
-
-    conda "conda-forge::python=3.9.5"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'biocontainers/python:3.9--1' }"
-
-    input:
-    path fasta
-    path gtf
-    path add_fasta
-    val  biotype
-
-    output:
-    path "${name}.fasta", emit: fasta
-    path "${name}.gtf"  , emit: gtf
-    path "versions.yml" , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def genome_name  = params.genome ? params.genome : fasta.getBaseName()
-    def biotype_name = biotype ? "-b $biotype" : ''
-    def add_name     = add_fasta.getBaseName()
-    name             = "${genome_name}_${add_name}"
-    """
-    fasta2gtf.py \\
-        -o ${add_fasta.baseName}.gtf \\
-        $biotype_name \\
-        $add_fasta
-
-    cat $fasta $add_fasta > ${name}.fasta
-    cat $gtf ${add_fasta.baseName}.gtf > ${name}.gtf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/deseq2_qc/environment.yml b/modules/local/deseq2_qc/environment.yml
new file mode 100644
index 000000000..9daad310d
--- /dev/null
+++ b/modules/local/deseq2_qc/environment.yml
@@ -0,0 +1,15 @@
+name: deseq2_qc
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::r-base
+  - conda-forge::r-optparse
+  - conda-forge::r-ggplot2
+  - conda-forge::r-rcolorbrewer
+  - conda-forge::r-pheatmap
+  - bioconda::bioconductor-deseq2
+  - bioconda::bioconductor-biocparallel
+  - bioconda::bioconductor-tximport
+  - bioconda::bioconductor-complexheatmap
diff --git a/modules/local/deseq2_qc/main.nf b/modules/local/deseq2_qc/main.nf
index 466194934..7aa81e9b5 100644
--- a/modules/local/deseq2_qc/main.nf
+++ b/modules/local/deseq2_qc/main.nf
@@ -3,7 +3,7 @@ process DESEQ2_QC {
 
     // (Bio)conda packages have intentionally not been pinned to a specific version
     // This was to avoid the pipeline failing due to package conflicts whilst creating the environment when using -profile conda
-    conda "conda-forge::r-base bioconda::bioconductor-deseq2 bioconda::bioconductor-biocparallel bioconda::bioconductor-tximport bioconda::bioconductor-complexheatmap conda-forge::r-optparse conda-forge::r-ggplot2 conda-forge::r-rcolorbrewer conda-forge::r-pheatmap"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' :
         'biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }"
@@ -57,4 +57,31 @@ process DESEQ2_QC {
         bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
     END_VERSIONS
     """
+
+    stub:
+    def args2 = task.ext.args2 ?: ''
+    def label_lower = args2.toLowerCase()
+    prefix = task.ext.prefix ?: "deseq2"
+    """
+    touch ${label_lower}.pca.vals_mqc.tsv
+    touch ${label_lower}.sample.dists_mqc.tsv
+    touch ${prefix}.dds.RData
+    touch ${prefix}.pca.vals.txt
+    touch ${prefix}.plots.pdf
+    touch ${prefix}.sample.dists.txt
+    touch R_sessionInfo.log
+
+    mkdir size_factors
+    touch size_factors/${prefix}.size_factors.RData
+    for i in `head $counts -n 1 | cut -f3-`;
+    do
+        touch size_factors/\${i}.size_factors.RData
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+        bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/deseq2_qc/tests/main.nf.test b/modules/local/deseq2_qc/tests/main.nf.test
new file mode 100644
index 000000000..a9d35997d
--- /dev/null
+++ b/modules/local/deseq2_qc/tests/main.nf.test
@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process DESEQ2_QC"
+    script "../main.nf"
+    process "DESEQ2_QC"
+
+    test("parse count data correctly") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.pipelines_testdata_base_path + "deseq2qc/countFile.tsv", checkIfExists: true)
+                input[1] = file(params.pipelines_testdata_base_path + "deseq2qc/deseq2_pca_header.txt", checkIfExists: true)
+                input[2] = file(params.pipelines_testdata_base_path + "deseq2qc/deseq2_clustering_header.txt", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.dists_multiqc,
+                    process.out.dists_txt,
+                    process.out.log,
+                    process.out.pca_multiqc,
+                    process.out.pca_txt,
+                    process.out.rdata,
+                    process.out.size_factors,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("parse count data correctly - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = file(params.pipelines_testdata_base_path + "deseq2qc/countFile.tsv", checkIfExists: true)
+                input[1] = file(params.pipelines_testdata_base_path + "deseq2qc/deseq2_pca_header.txt", checkIfExists: true)
+                input[2] = file(params.pipelines_testdata_base_path + "deseq2qc/deseq2_clustering_header.txt", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/deseq2_qc/tests/main.nf.test.snap b/modules/local/deseq2_qc/tests/main.nf.test.snap
new file mode 100644
index 000000000..1c6bc7105
--- /dev/null
+++ b/modules/local/deseq2_qc/tests/main.nf.test.snap
@@ -0,0 +1,121 @@
+{
+    "parse count data correctly - stub": {
+        "content": [
+            {
+                "0": [
+                    "deseq2.plots.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "deseq2.dds.RData:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "deseq2.pca.vals.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "3": [
+
+                ],
+                "4": [
+                    "deseq2.sample.dists.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "5": [
+
+                ],
+                "6": [
+                    "R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "7": [
+                    [
+                        "RAP1_IAA_30M_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "RAP1_UNINDUCED_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "RAP1_UNINDUCED_REP2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "WT_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "WT_REP2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "deseq2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    "versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
+                ],
+                "dists_multiqc": [
+
+                ],
+                "dists_txt": [
+                    "deseq2.sample.dists.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "log": [
+                    "R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "pca_multiqc": [
+
+                ],
+                "pca_txt": [
+                    "deseq2.pca.vals.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "pdf": [
+                    "deseq2.plots.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "rdata": [
+                    "deseq2.dds.RData:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "size_factors": [
+                    [
+                        "RAP1_IAA_30M_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "RAP1_UNINDUCED_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "RAP1_UNINDUCED_REP2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "WT_REP1.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "WT_REP2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "deseq2.size_factors.RData:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T11:38:08.92794"
+    },
+    "parse count data correctly": {
+        "content": [
+            [
+
+            ],
+            [
+                "deseq2.sample.dists.txt:md5,1616ce40eb58ee75640efed219c6bbec"
+            ],
+            [
+                "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676"
+            ],
+            [
+
+            ],
+            [
+                "deseq2.pca.vals.txt:md5,4cda8e32ec39326c1350e77b4b607aad"
+            ],
+            [
+                "deseq2.dds.RData:md5,c7c1872e7566321d0c3f7ca56c463088"
+            ],
+            [
+                [
+                    "RAP1_IAA_30M_REP1.txt:md5,ce4ff0b74aeedc3dc12a764c3504c9df",
+                    "RAP1_UNINDUCED_REP1.txt:md5,51c9b23be5e82670aceb14f7e58dd867",
+                    "RAP1_UNINDUCED_REP2.txt:md5,2c56106abcd9d31980f672b6e2862ee8",
+                    "WT_REP1.txt:md5,5e3fe5f7e9b7f300be43649a8b496352",
+                    "WT_REP2.txt:md5,2ce093f2c2e92c1bde1cd3da91ac884c",
+                    "deseq2.size_factors.RData:md5,51c6643a0f8a9edabbff8df0165451f2"
+                ]
+            ],
+            [
+                "versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T11:21:20.349616"
+    }
+}
diff --git a/modules/local/dupradar/main.nf b/modules/local/dupradar/main.nf
deleted file mode 100644
index 9f9152d1e..000000000
--- a/modules/local/dupradar/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-process DUPRADAR {
-    tag "$meta.id"
-    label 'process_long'
-
-    conda "bioconda::bioconductor-dupradar=1.28.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dupradar:1.28.0--r42hdfd78af_0' :
-        'biocontainers/bioconductor-dupradar:1.28.0--r42hdfd78af_0' }"
-
-    input:
-    tuple val(meta), path(bam)
-    path  gtf
-
-    output:
-    tuple val(meta), path("*.pdf")    , emit: pdf
-    tuple val(meta), path("*.txt")    , emit: txt
-    tuple val(meta), path("*_mqc.txt"), emit: multiqc
-    path "versions.yml"               , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    def strandedness = 0
-    if (meta.strandedness == 'forward') {
-        strandedness = 1
-    } else if (meta.strandedness == 'reverse') {
-        strandedness = 2
-    }
-    def paired_end = meta.single_end ? 'single' :  'paired'
-    """
-    dupradar.r \\
-        $bam \\
-        $prefix \\
-        $gtf \\
-        $strandedness \\
-        $paired_end \\
-        $task.cpus
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        bioconductor-dupradar: \$(Rscript -e "library(dupRadar); cat(as.character(packageVersion('dupRadar')))")
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/local/gtf2bed/environment.yml
similarity index 51%
rename from modules/nf-core/custom/dumpsoftwareversions/environment.yml
rename to modules/local/gtf2bed/environment.yml
index f0c63f698..3c009b31b 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml
+++ b/modules/local/gtf2bed/environment.yml
@@ -1,7 +1,7 @@
-name: custom_dumpsoftwareversions
+name: gtf2bed
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.17
+  - conda-forge::perl=5.26.2
diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf
index 8a4bae8ff..a2523c9cf 100644
--- a/modules/local/gtf2bed/main.nf
+++ b/modules/local/gtf2bed/main.nf
@@ -2,7 +2,7 @@ process GTF2BED {
     tag "$gtf"
     label 'process_low'
 
-    conda "conda-forge::perl=5.26.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
         'biocontainers/perl:5.26.2' }"
@@ -28,4 +28,14 @@ process GTF2BED {
         perl: \$(echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${gtf.baseName}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        perl: \$(echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/gtf2bed/tests/main.nf.test b/modules/local/gtf2bed/tests/main.nf.test
new file mode 100644
index 000000000..b640d2053
--- /dev/null
+++ b/modules/local/gtf2bed/tests/main.nf.test
@@ -0,0 +1,44 @@
+nextflow_process {
+
+    name "Test Process GTF2BED"
+    script "../main.nf"
+    process "GTF2BED"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/gtf2bed/tests/main.nf.test.snap b/modules/local/gtf2bed/tests/main.nf.test.snap
new file mode 100644
index 000000000..66ec3bf9e
--- /dev/null
+++ b/modules/local/gtf2bed/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "versions.yml:md5,d04d815c224b980b6f3818d4b2fd4fe3"
+                ],
+                "bed": [
+                    "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,d04d815c224b980b6f3818d4b2fd4fe3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T11:46:28.123826"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            {
+                "0": [
+                    "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "versions.yml:md5,d04d815c224b980b6f3818d4b2fd4fe3"
+                ],
+                "bed": [
+                    "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,d04d815c224b980b6f3818d4b2fd4fe3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-07T15:00:44.458214"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/gtf_filter/environment.yml b/modules/local/gtf_filter/environment.yml
new file mode 100644
index 000000000..c8b5ca202
--- /dev/null
+++ b/modules/local/gtf_filter/environment.yml
@@ -0,0 +1,7 @@
+name: gtf_filter
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::python=3.9.5
diff --git a/modules/local/gtf_filter/main.nf b/modules/local/gtf_filter/main.nf
index d14e8ff42..60eb9a9bd 100644
--- a/modules/local/gtf_filter/main.nf
+++ b/modules/local/gtf_filter/main.nf
@@ -1,7 +1,7 @@
 process GTF_FILTER {
     tag "$fasta"
 
-    conda "conda-forge::python=3.9.5"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'biocontainers/python:3.9--1' }"
@@ -29,4 +29,14 @@ process GTF_FILTER {
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${fasta.baseName}.filtered.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/gtf_filter/tests/main.nf.test b/modules/local/gtf_filter/tests/main.nf.test
new file mode 100644
index 000000000..324ee6bb9
--- /dev/null
+++ b/modules/local/gtf_filter/tests/main.nf.test
@@ -0,0 +1,46 @@
+nextflow_process {
+
+    name "Test Process GTF_FILTER"
+    script "../main.nf"
+    process "GTF_FILTER"
+
+    test("sarscov2 - fasta - gtf") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - fasta - gtf - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/gtf_filter/tests/main.nf.test.snap b/modules/local/gtf_filter/tests/main.nf.test.snap
new file mode 100644
index 000000000..d22a4fa5b
--- /dev/null
+++ b/modules/local/gtf_filter/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+    "sarscov2 - fasta - gtf": {
+        "content": [
+            {
+                "0": [
+                    "genome.filtered.gtf:md5,aa8b2aa1e0b5fbbba3b04d471e1b0535"
+                ],
+                "1": [
+                    "versions.yml:md5,4adf55ec05d247fd6d253459bd80856f"
+                ],
+                "genome_gtf": [
+                    "genome.filtered.gtf:md5,aa8b2aa1e0b5fbbba3b04d471e1b0535"
+                ],
+                "versions": [
+                    "versions.yml:md5,4adf55ec05d247fd6d253459bd80856f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T11:47:56.314297"
+    },
+    "sarscov2 - fasta - gtf - stub": {
+        "content": [
+            {
+                "0": [
+                    "genome.filtered.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "versions.yml:md5,4adf55ec05d247fd6d253459bd80856f"
+                ],
+                "genome_gtf": [
+                    "genome.filtered.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,4adf55ec05d247fd6d253459bd80856f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T11:48:19.085835"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/multiqc/main.nf b/modules/local/multiqc/main.nf
deleted file mode 100644
index be0dfe2c3..000000000
--- a/modules/local/multiqc/main.nf
+++ /dev/null
@@ -1,74 +0,0 @@
-process MULTIQC {
-    label 'process_medium'
-
-    conda "bioconda::multiqc=1.19"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.19--pyhdfd78af_0' }"
-
-    input:
-    path multiqc_config
-    path multiqc_custom_config
-    path software_versions
-    path workflow_summary
-    path methods_description
-    path logo
-    path fail_trimming_summary
-    path fail_mapping_summary
-    path fail_strand_check
-    path ('fastqc/raw/*')
-    path ('fastqc/trim/*')
-    path ('trim_log/*')
-    path ('sortmerna/*')
-    path ('star/*')
-    path ('hisat2/*')
-    path ('rsem/*')
-    path ('pseudoalignment/*')
-    path ('samtools/stats/*')
-    path ('samtools/flagstat/*')
-    path ('samtools/idxstats/*')
-    path ('picard/markduplicates/*')
-    path ('featurecounts/*')
-    path ('deseq2/aligner/*')
-    path ('deseq2/aligner/*')
-    path ('deseq2/pseudoaligner/*')
-    path ('deseq2/pseudoaligner/*')
-    path ('preseq/*')
-    path ('qualimap/*')
-    path ('dupradar/*')
-    path ('rseqc/bam_stat/*')
-    path ('rseqc/infer_experiment/*')
-    path ('rseqc/inner_distance/*')
-    path ('rseqc/junction_annotation/*')
-    path ('rseqc/junction_saturation/*')
-    path ('rseqc/read_distribution/*')
-    path ('rseqc/read_duplication/*')
-    path ('rseqc/tin/*')
-
-    output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
-    prefix = task.ext.prefix ?: "multiqc_report"
-    """
-    multiqc \\
-        -n ${prefix}.html \\
-        -f \\
-        $args \\
-        $custom_config \\
-        .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/multiqc_custom_biotype/environment.yml b/modules/local/multiqc_custom_biotype/environment.yml
new file mode 100644
index 000000000..7a6b5722e
--- /dev/null
+++ b/modules/local/multiqc_custom_biotype/environment.yml
@@ -0,0 +1,7 @@
+name: multiqc_custom_biotype
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::python=3.9.5
diff --git a/modules/local/multiqc_custom_biotype/main.nf b/modules/local/multiqc_custom_biotype/main.nf
index 9c0fe94eb..a4b923c3e 100644
--- a/modules/local/multiqc_custom_biotype/main.nf
+++ b/modules/local/multiqc_custom_biotype/main.nf
@@ -1,7 +1,7 @@
 process MULTIQC_CUSTOM_BIOTYPE {
     tag "$meta.id"
 
-    conda "conda-forge::python=3.9.5"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'biocontainers/python:3.9--1' }"
@@ -33,4 +33,16 @@ process MULTIQC_CUSTOM_BIOTYPE {
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.biotype_counts_mqc.tsv
+    touch ${prefix}.biotype_counts_rrna_mqc.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/multiqc_custom_biotype/nextflow.config b/modules/local/multiqc_custom_biotype/nextflow.config
new file mode 100644
index 000000000..68fecaa66
--- /dev/null
+++ b/modules/local/multiqc_custom_biotype/nextflow.config
@@ -0,0 +1,13 @@
+if (!params.skip_alignment && !params.skip_qc) {
+    if (!params.skip_biotype_qc && params.featurecounts_group_type) {
+        process {
+            withName: 'MULTIQC_CUSTOM_BIOTYPE' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+}
diff --git a/modules/local/multiqc_custom_biotype/tests/main.nf.test b/modules/local/multiqc_custom_biotype/tests/main.nf.test
new file mode 100644
index 000000000..bd6cde6bc
--- /dev/null
+++ b/modules/local/multiqc_custom_biotype/tests/main.nf.test
@@ -0,0 +1,56 @@
+nextflow_process {
+
+    name "Test Process MULTIQC_CUSTOM_BIOTYPE"
+    script "../main.nf"
+    process "MULTIQC_CUSTOM_BIOTYPE"
+
+    test("test sarscov2 count data succesfully completes") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id: 'test' ],
+                        file(params.pipelines_testdata_base_path + 'multiqc_custom_biotype/test.featureCounts.txt', checkIfExists: true)
+                    ]
+                )
+                input[1] = file(params.pipelines_testdata_base_path + 'multiqc_custom_biotype/biotypes_header.txt', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success},
+                { assert snapshot(process.out).match()}
+            )
+        }
+    }
+
+    test("test sarscov2 count data - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id: 'test' ],
+                        file(params.pipelines_testdata_base_path + 'multiqc_custom_biotype/test.featureCounts.txt', checkIfExists: true)
+                    ]
+                )
+                input[1] = file(params.pipelines_testdata_base_path + 'multiqc_custom_biotype/biotypes_header.txt', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success},
+                { assert snapshot(process.out).match()}
+            )
+        }
+    }
+}
diff --git a/modules/local/multiqc_custom_biotype/tests/main.nf.test.snap b/modules/local/multiqc_custom_biotype/tests/main.nf.test.snap
new file mode 100644
index 000000000..2fc5e4ab6
--- /dev/null
+++ b/modules/local/multiqc_custom_biotype/tests/main.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "test sarscov2 count data succesfully completes": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.biotype_counts_mqc.tsv:md5,d996f27aeec64370cade26717aa22e1e",
+                            "test.biotype_counts_rrna_mqc.tsv:md5,31c68d05ffe90d1e3eb2cb2ef9a7b4d9"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,575b3b4c8a8a6e508c8ceeca41331b6b"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.biotype_counts_mqc.tsv:md5,d996f27aeec64370cade26717aa22e1e",
+                            "test.biotype_counts_rrna_mqc.tsv:md5,31c68d05ffe90d1e3eb2cb2ef9a7b4d9"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,575b3b4c8a8a6e508c8ceeca41331b6b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T16:48:24.844934"
+    },
+    "test sarscov2 count data - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.biotype_counts_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.biotype_counts_rrna_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,575b3b4c8a8a6e508c8ceeca41331b6b"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.biotype_counts_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.biotype_counts_rrna_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,575b3b4c8a8a6e508c8ceeca41331b6b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T11:50:15.104113"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/preprocess_transcripts_fasta_gencode/environment.yml b/modules/local/preprocess_transcripts_fasta_gencode/environment.yml
new file mode 100644
index 000000000..06e4d9658
--- /dev/null
+++ b/modules/local/preprocess_transcripts_fasta_gencode/environment.yml
@@ -0,0 +1,7 @@
+name: preprocess_transcripts_fasta_gencode
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
diff --git a/modules/local/preprocess_transcripts_fasta_gencode/main.nf b/modules/local/preprocess_transcripts_fasta_gencode/main.nf
index 41f1d42f6..2722e66c7 100644
--- a/modules/local/preprocess_transcripts_fasta_gencode/main.nf
+++ b/modules/local/preprocess_transcripts_fasta_gencode/main.nf
@@ -1,7 +1,7 @@
 process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE {
     tag "$fasta"
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"
@@ -28,4 +28,16 @@ process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE {
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def gzipped = fasta.toString().endsWith('.gz')
+    def outfile = gzipped ? file(fasta.baseName).baseName : fasta.baseName
+    """
+    touch ${outfile}.fixed.fa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/preprocess_transcripts_fasta_gencode/tests/main.nf.test b/modules/local/preprocess_transcripts_fasta_gencode/tests/main.nf.test
new file mode 100644
index 000000000..b07b4c001
--- /dev/null
+++ b/modules/local/preprocess_transcripts_fasta_gencode/tests/main.nf.test
@@ -0,0 +1,60 @@
+nextflow_process {
+
+    name "Test Process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE"
+    script "../main.nf"
+    process "PREPROCESS_TRANSCRIPTS_FASTA_GENCODE"
+
+    test("gencode fasta") {
+
+        when {
+            process {
+                """
+                def fileContents = [
+                    '>chr22|removeme',
+                    'ACTCAAGATAATGATGAGTAAAGAATATATTTCTAACAACAAAAAGGAAATTTGATAGTA'
+                ]
+                def gencodeFasta = file("${workDir}/gencodeFasta.fasta")
+                gencodeFasta.withWriter{ out ->
+                    fileContents.each {out.println it}
+                }
+                input[0] = gencodeFasta
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("gencode fasta - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                def fileContents = [
+                    '>chr22|removeme',
+                    'ACTCAAGATAATGATGAGTAAAGAATATATTTCTAACAACAAAAAGGAAATTTGATAGTA'
+                ]
+                def gencodeFasta = file("${workDir}/gencodeFasta.fasta")
+                gencodeFasta.withWriter{ out ->
+                    fileContents.each {out.println it}
+                }
+                input[0] = gencodeFasta
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/preprocess_transcripts_fasta_gencode/tests/main.nf.test.snap b/modules/local/preprocess_transcripts_fasta_gencode/tests/main.nf.test.snap
new file mode 100644
index 000000000..eaef85b1b
--- /dev/null
+++ b/modules/local/preprocess_transcripts_fasta_gencode/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+    "gencode fasta": {
+        "content": [
+            {
+                "0": [
+                    "gencodeFasta.fixed.fa:md5,e9267fa40efc784cc92575b5ba8a441b"
+                ],
+                "1": [
+                    "versions.yml:md5,e2c7f636c472887a914b128d1444737e"
+                ],
+                "fasta": [
+                    "gencodeFasta.fixed.fa:md5,e9267fa40efc784cc92575b5ba8a441b"
+                ],
+                "versions": [
+                    "versions.yml:md5,e2c7f636c472887a914b128d1444737e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T16:16:36.494744"
+    },
+    "gencode fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    "gencodeFasta.fixed.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "versions.yml:md5,e2c7f636c472887a914b128d1444737e"
+                ],
+                "fasta": [
+                    "gencodeFasta.fixed.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,e2c7f636c472887a914b128d1444737e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T11:54:20.291494"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/rsem_merge_counts/environment.yml b/modules/local/rsem_merge_counts/environment.yml
new file mode 100644
index 000000000..eeeb3329a
--- /dev/null
+++ b/modules/local/rsem_merge_counts/environment.yml
@@ -0,0 +1,7 @@
+name: rsem_merge_counts
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
diff --git a/modules/local/rsem_merge_counts/main.nf b/modules/local/rsem_merge_counts/main.nf
index 3f226f54d..c220e31de 100644
--- a/modules/local/rsem_merge_counts/main.nf
+++ b/modules/local/rsem_merge_counts/main.nf
@@ -1,7 +1,7 @@
 process RSEM_MERGE_COUNTS {
     label "process_medium"
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"
@@ -52,4 +52,17 @@ process RSEM_MERGE_COUNTS {
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch rsem.merged.gene_counts.tsv
+    touch rsem.merged.gene_tpm.tsv
+    touch rsem.merged.transcript_counts.tsv
+    touch rsem.merged.transcript_tpm.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/rsem_merge_counts/tests/main.nf.test b/modules/local/rsem_merge_counts/tests/main.nf.test
new file mode 100644
index 000000000..61008082a
--- /dev/null
+++ b/modules/local/rsem_merge_counts/tests/main.nf.test
@@ -0,0 +1,62 @@
+nextflow_process {
+
+    name "Test Process RSEM_MERGE_COUNTS"
+    script "../main.nf"
+    process "RSEM_MERGE_COUNTS"
+
+    test("Should run without failures") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_IAA_30M_REP1.genes.results", checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP1.genes.results", checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP2.genes.results", checkIfExists: true)
+                ]).collect()
+                input[1] = Channel.of([
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_IAA_30M_REP1.isoforms.results", checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP1.isoforms.results", checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP2.isoforms.results", checkIfExists: true)
+                ]).collect()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_IAA_30M_REP1.genes.results", checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP1.genes.results", checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP2.genes.results", checkIfExists: true)
+                ]).collect()
+                input[1] = Channel.of([
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_IAA_30M_REP1.isoforms.results", checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP1.isoforms.results", checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP2.isoforms.results", checkIfExists: true)
+                ]).collect()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/rsem_merge_counts/tests/main.nf.test.snap b/modules/local/rsem_merge_counts/tests/main.nf.test.snap
new file mode 100644
index 000000000..1715d1279
--- /dev/null
+++ b/modules/local/rsem_merge_counts/tests/main.nf.test.snap
@@ -0,0 +1,84 @@
+{
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "3": [
+                    "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "4": [
+                    "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
+                ],
+                "counts_gene": [
+                    "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "counts_transcript": [
+                    "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "tpm_gene": [
+                    "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "tpm_transcript": [
+                    "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T11:55:29.45389"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "rsem.merged.gene_counts.tsv:md5,7d1da94077dc2f90cfb2c793ca5b7446"
+                ],
+                "1": [
+                    "rsem.merged.gene_tpm.tsv:md5,39bad606eb012456bba1d995fe0feb5f"
+                ],
+                "2": [
+                    "rsem.merged.transcript_counts.tsv:md5,e40bba0aafc5904361513b3513c217ad"
+                ],
+                "3": [
+                    "rsem.merged.transcript_tpm.tsv:md5,abbaac45f9938716c58d604299ea284e"
+                ],
+                "4": [
+                    "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
+                ],
+                "counts_gene": [
+                    "rsem.merged.gene_counts.tsv:md5,7d1da94077dc2f90cfb2c793ca5b7446"
+                ],
+                "counts_transcript": [
+                    "rsem.merged.transcript_counts.tsv:md5,e40bba0aafc5904361513b3513c217ad"
+                ],
+                "tpm_gene": [
+                    "rsem.merged.gene_tpm.tsv:md5,39bad606eb012456bba1d995fe0feb5f"
+                ],
+                "tpm_transcript": [
+                    "rsem.merged.transcript_tpm.tsv:md5,abbaac45f9938716c58d604299ea284e"
+                ],
+                "versions": [
+                    "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-09T17:13:37.377348"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/star_align_igenomes/environment.yml b/modules/local/star_align_igenomes/environment.yml
new file mode 100644
index 000000000..0d92f8dd5
--- /dev/null
+++ b/modules/local/star_align_igenomes/environment.yml
@@ -0,0 +1,9 @@
+name: star_align_igenomes
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::star=2.6.1d
+  - bioconda::samtools=1.10
+  - conda-forge::gawk=5.1.0
diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf
index b412a7e5c..7bda3df84 100644
--- a/modules/local/star_align_igenomes/main.nf
+++ b/modules/local/star_align_igenomes/main.nf
@@ -2,13 +2,13 @@ process STAR_ALIGN_IGENOMES {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
         'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads, stageAs: "input*/*")
     tuple val(meta2), path(index)
     tuple val(meta3), path(gtf)
     val star_ignore_sjdbgtf
@@ -16,12 +16,12 @@ process STAR_ALIGN_IGENOMES {
     val seq_center
 
     output:
-    tuple val(meta), path('*d.out.bam')       , emit: bam
     tuple val(meta), path('*Log.final.out')   , emit: log_final
     tuple val(meta), path('*Log.out')         , emit: log_out
     tuple val(meta), path('*Log.progress.out'), emit: log_progress
     path  "versions.yml"                      , emit: versions
 
+    tuple val(meta), path('*d.out.bam')              , optional:true, emit: bam
     tuple val(meta), path('*sortedByCoord.out.bam')  , optional:true, emit: bam_sorted
     tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript
     tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted
@@ -36,6 +36,8 @@ process STAR_ALIGN_IGENOMES {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def reads1 = [], reads2 = []
+    meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
     def ignore_gtf      = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
     def seq_platform    = seq_platform ? "'PL:$seq_platform'" : ""
     def seq_center      = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
@@ -44,7 +46,7 @@ process STAR_ALIGN_IGENOMES {
     """
     STAR \\
         --genomeDir $index \\
-        --readFilesIn $reads  \\
+        --readFilesIn ${reads1.join(",")} ${reads2.join(",")} \\
         --runThreadN $task.cpus \\
         --outFileNamePrefix $prefix. \\
         $out_sam_type \\
@@ -70,4 +72,33 @@ process STAR_ALIGN_IGENOMES {
         gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}.unmapped_1.fastq.gz
+    echo "" | gzip > ${prefix}.unmapped_2.fastq.gz
+    touch ${prefix}Xd.out.bam
+    touch ${prefix}.Log.final.out
+    touch ${prefix}.Log.out
+    touch ${prefix}.Log.progress.out
+    touch ${prefix}.sortedByCoord.out.bam
+    touch ${prefix}.toTranscriptome.out.bam
+    touch ${prefix}.Aligned.unsort.out.bam
+    touch ${prefix}.Aligned.sortedByCoord.out.bam
+    touch ${prefix}.tab
+    touch ${prefix}.SJ.out.tab
+    touch ${prefix}.ReadsPerGene.out.tab
+    touch ${prefix}.Chimeric.out.junction
+    touch ${prefix}.out.sam
+    touch ${prefix}.Signal.UniqueMultiple.str1.out.wig
+    touch ${prefix}.Signal.UniqueMultiple.str1.out.bg
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        star: \$(STAR --version | sed -e "s/STAR_//g")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/star_align_igenomes/tests/main.nf.test b/modules/local/star_align_igenomes/tests/main.nf.test
new file mode 100644
index 000000000..37f65930a
--- /dev/null
+++ b/modules/local/star_align_igenomes/tests/main.nf.test
@@ -0,0 +1,534 @@
+nextflow_process {
+
+    name "Test Process STAR_ALIGN_IGENOMES"
+    script "../main.nf"
+    process "STAR_ALIGN_IGENOMES"
+
+    test("homo_sapiens - single_end") {
+        config "./nextflow.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end") {
+        config "./nextflow.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - arriba") {
+        config "./nextflow.arriba.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - starfusion") {
+        config "./nextflow.starfusion.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - multiple") {
+        config "./nextflow.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - single_end - stub") {
+        options "-stub"
+        config "./nextflow.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - stub") {
+        options "-stub"
+        config "./nextflow.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - arriba - stub") {
+        options "-stub"
+        config "./nextflow.arriba.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - starfusion - stub") {
+        options "-stub"
+        config "./nextflow.starfusion.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - multiple - stub") {
+        options "-stub"
+        config "./nextflow.config"
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/star_align_igenomes/tests/main.nf.test.snap b/modules/local/star_align_igenomes/tests/main.nf.test.snap
new file mode 100644
index 000000000..5a0b193b1
--- /dev/null
+++ b/modules/local/star_align_igenomes/tests/main.nf.test.snap
@@ -0,0 +1,1522 @@
+{
+    "homo_sapiens - single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,957a57604ceb366b7af0123738e13559"
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
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+                        "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tab": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,957a57604ceb366b7af0123738e13559"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:14:00.135162"
+    },
+    "homo_sapiens - paired_end - multiple": {
+        "content": [
+            "test.Log.final.out",
+            "test.Log.out",
+            "test.Log.progress.out",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,7b20152380dbc52ec23d2e95a7953710"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,7b20152380dbc52ec23d2e95a7953710"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            null,
+            [
+                
+            ],
+            [
+                
+            ],
+            null,
+            [
+                
+            ],
+            null,
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,069877e053714e23010fe4e1c003b4a2"
+                ]
+            ],
+            null,
+            [
+                "versions.yml:md5,957a57604ceb366b7af0123738e13559"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:12:16.618713"
+    },
+    "homo_sapiens - paired_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,957a57604ceb366b7af0123738e13559"
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam_sorted": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam_transcript": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_unsorted": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "junction": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log_final": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log_out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log_progress": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tab": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,957a57604ceb366b7af0123738e13559"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:12:56.326797"
+    },
+    "homo_sapiens - paired_end - starfusion": {
+        "content": [
+            "test.Log.final.out",
+            "test.Log.out",
+            "test.Log.progress.out",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.out.bam:md5,7806e69c537f72e494f9ce8e95f16355"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            null,
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Chimeric.out.junction:md5,c6d4d8c641ebb1c152a10da44f0dbf20"
+                ]
+            ],
+            null,
+            [
+                
+            ],
+            null,
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,19c3faa1bfa9a0cc5e4c45f17065b53a"
+                ]
+            ],
+            null,
+            [
+                "versions.yml:md5,957a57604ceb366b7af0123738e13559"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:10:49.022723"
+    },
+    "homo_sapiens - paired_end - arriba": {
+        "content": [
+            "test.Log.final.out",
+            "test.Log.out",
+            "test.Log.progress.out",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.out.bam:md5,28ecaa85a5dec1a18c877c85d874adf2"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            null,
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Chimeric.out.junction:md5,62760fd60371d5bacae324c370358944"
+                ]
+            ],
+            null,
+            [
+                
+            ],
+            null,
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,5155c9fd1f787ad6d7d80987fb06219c"
+                ]
+            ],
+            null,
+            [
+                "versions.yml:md5,957a57604ceb366b7af0123738e13559"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:07:19.724256"
+    },
+    "homo_sapiens - paired_end - starfusion - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,957a57604ceb366b7af0123738e13559"
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam_sorted": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam_transcript": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_unsorted": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "junction": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log_final": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log_out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log_progress": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tab": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,957a57604ceb366b7af0123738e13559"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:13:37.606866"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/star_align_igenomes/tests/nextflow.arriba.config b/modules/local/star_align_igenomes/tests/nextflow.arriba.config
new file mode 100644
index 000000000..ece3c0cbf
--- /dev/null
+++ b/modules/local/star_align_igenomes/tests/nextflow.arriba.config
@@ -0,0 +1,14 @@
+process {
+
+    withName: STAR_GENOMEGENERATE_IGENOMES {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: STAR_ALIGN_IGENOMES {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50 --chimOutType Junctions'
+    }
+
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/modules/local/star_align_igenomes/tests/nextflow.config b/modules/local/star_align_igenomes/tests/nextflow.config
new file mode 100644
index 000000000..7c663e414
--- /dev/null
+++ b/modules/local/star_align_igenomes/tests/nextflow.config
@@ -0,0 +1,14 @@
+process {
+
+    withName: STAR_GENOMEGENERATE_IGENOMES {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: STAR_ALIGN_IGENOMES {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded'
+    }
+
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/modules/local/star_align_igenomes/tests/nextflow.starfusion.config b/modules/local/star_align_igenomes/tests/nextflow.starfusion.config
new file mode 100644
index 000000000..922520ca2
--- /dev/null
+++ b/modules/local/star_align_igenomes/tests/nextflow.starfusion.config
@@ -0,0 +1,14 @@
+process {
+
+    withName: STAR_GENOMEGENERATE_IGENOMES {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: STAR_ALIGN_IGENOMES {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outReadsUnmapped None --twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30'
+    }
+
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/modules/local/star_genomegenerate_igenomes/environment.yml b/modules/local/star_genomegenerate_igenomes/environment.yml
new file mode 100644
index 000000000..c3c6c2481
--- /dev/null
+++ b/modules/local/star_genomegenerate_igenomes/environment.yml
@@ -0,0 +1,9 @@
+name: star_genomegenerate_igenomes
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::star=2.6.1d
+  - bioconda::samtools=1.10
+  - conda-forge::gawk=5.1.0
diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf
index 7766faaaf..4e2fcf6bf 100644
--- a/modules/local/star_genomegenerate_igenomes/main.nf
+++ b/modules/local/star_genomegenerate_igenomes/main.nf
@@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES {
     tag "$fasta"
     label 'process_high'
 
-    conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
         'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
@@ -22,6 +22,7 @@ process STAR_GENOMEGENERATE_IGENOMES {
     def args = task.ext.args ?: ''
     def args_list = args.tokenize()
     def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+    def include_gtf = gtf ? "--sjdbGTFfile $gtf" : ''
     if (args_list.contains('--genomeSAindexNbases')) {
         """
         mkdir star
@@ -29,7 +30,7 @@ process STAR_GENOMEGENERATE_IGENOMES {
             --runMode genomeGenerate \\
             --genomeDir star/ \\
             --genomeFastaFiles $fasta \\
-            --sjdbGTFfile $gtf \\
+            $include_gtf \\
             --runThreadN $task.cpus \\
             $memory \\
             $args
@@ -51,7 +52,7 @@ process STAR_GENOMEGENERATE_IGENOMES {
             --runMode genomeGenerate \\
             --genomeDir star/ \\
             --genomeFastaFiles $fasta \\
-            --sjdbGTFfile $gtf \\
+            $include_gtf \\
             --runThreadN $task.cpus \\
             --genomeSAindexNbases \$NUM_BASES \\
             $memory \\
@@ -65,4 +66,54 @@ process STAR_GENOMEGENERATE_IGENOMES {
         END_VERSIONS
         """
     }
+
+    stub:
+    if (gtf) {
+        """
+        mkdir star
+        touch star/Genome
+        touch star/Log.out
+        touch star/SA
+        touch star/SAindex
+        touch star/chrLength.txt
+        touch star/chrName.txt
+        touch star/chrNameLength.txt
+        touch star/chrStart.txt
+        touch star/exonGeTrInfo.tab
+        touch star/exonInfo.tab
+        touch star/geneInfo.tab
+        touch star/genomeParameters.txt
+        touch star/sjdbInfo.txt
+        touch star/sjdbList.fromGTF.out.tab
+        touch star/sjdbList.out.tab
+        touch star/transcriptInfo.tab
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            star: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+        END_VERSIONS
+        """
+    } else {
+        """
+        mkdir star
+        touch star/Genome
+        touch star/Log.out
+        touch star/SA
+        touch star/SAindex
+        touch star/chrLength.txt
+        touch star/chrName.txt
+        touch star/chrNameLength.txt
+        touch star/chrStart.txt
+        touch star/genomeParameters.txt
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            star: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+        END_VERSIONS
+        """
+    }
 }
diff --git a/modules/local/star_genomegenerate_igenomes/tests/main.nf.test b/modules/local/star_genomegenerate_igenomes/tests/main.nf.test
new file mode 100644
index 000000000..d3bd71891
--- /dev/null
+++ b/modules/local/star_genomegenerate_igenomes/tests/main.nf.test
@@ -0,0 +1,93 @@
+nextflow_process {
+
+    name "Test Process STAR_GENOMEGENERATE_IGENOMES"
+    script "../main.nf"
+    process "STAR_GENOMEGENERATE_IGENOMES"
+
+    test("fasta with gtf") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(),
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("fasta no gtf") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[1] = Channel.of([ ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(),
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("fasta with gtf - stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("fasta no gtf - stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[1] = Channel.of([ ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/star_genomegenerate_igenomes/tests/main.nf.test.snap b/modules/local/star_genomegenerate_igenomes/tests/main.nf.test.snap
new file mode 100644
index 000000000..1ba924611
--- /dev/null
+++ b/modules/local/star_genomegenerate_igenomes/tests/main.nf.test.snap
@@ -0,0 +1,128 @@
+{
+    "fasta with gtf": {
+        "content": [
+            "[]",
+            [
+                "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:14:17.250178"
+    },
+    "fasta no gtf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+                ],
+                "index": [
+                    [
+                        "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:15:09.671637"
+    },
+    "fasta no gtf": {
+        "content": [
+            "[]",
+            [
+                "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:14:35.674278"
+    },
+    "fasta with gtf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+                ],
+                "index": [
+                    [
+                        "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,562a70f12dd9e695449b59fbf604e98d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T20:14:52.732323"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/summarizedexperiment/main.nf b/modules/local/summarizedexperiment/main.nf
deleted file mode 100644
index f278e2301..000000000
--- a/modules/local/summarizedexperiment/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-process SUMMARIZEDEXPERIMENT {
-    tag "$tx2gene"
-    label "process_medium"
-
-    conda "bioconda::bioconductor-summarizedexperiment=1.24.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-summarizedexperiment:1.24.0--r41hdfd78af_0' :
-        'biocontainers/bioconductor-summarizedexperiment:1.24.0--r41hdfd78af_0' }"
-
-    input:
-    path counts
-    path tpm
-    path tx2gene
-
-    output:
-    path "*.rds"       , emit: rds
-    path "versions.yml", emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
-    """
-    summarizedexperiment.r \\
-        NULL \\
-        $counts \\
-        $tpm \\
-        $tx2gene
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        bioconductor-summarizedexperiment: \$(Rscript -e "library(SummarizedExperiment); cat(as.character(packageVersion('SummarizedExperiment')))")
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/tx2gene/main.nf b/modules/local/tx2gene/main.nf
deleted file mode 100644
index 150e74afb..000000000
--- a/modules/local/tx2gene/main.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-process TX2GENE {
-    tag "$gtf"
-    label "process_low"
-
-    conda "conda-forge::python=3.9.5"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'biocontainers/python:3.9--1' }"
-
-    input:
-    path ("quants/*")
-    val quant_type
-    path gtf
-
-    output:
-    path "*.tsv"       , emit: tsv
-    path "versions.yml", emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
-    """
-    tx2gene.py \\
-        --quant_type $quant_type \\
-        --gtf $gtf \\
-        --quants quants \\
-        --id $params.gtf_group_features \\
-        --extra $params.gtf_extra_attributes \\
-        -o tx2gene.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/tximport/main.nf b/modules/local/tximport/main.nf
deleted file mode 100644
index cd97d139f..000000000
--- a/modules/local/tximport/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-process TXIMPORT {
-    label "process_medium"
-
-    conda "bioconda::bioconductor-tximeta=1.12.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-tximeta:1.12.0--r41hdfd78af_0' :
-        'biocontainers/bioconductor-tximeta:1.12.0--r41hdfd78af_0' }"
-
-    input:
-    path ("quants/*")
-    path  tx2gene
-    val quant_type
-
-    output:
-    path "*gene_tpm.tsv"                 , emit: tpm_gene
-    path "*gene_counts.tsv"              , emit: counts_gene
-    path "*gene_counts_length_scaled.tsv", emit: counts_gene_length_scaled
-    path "*gene_counts_scaled.tsv"       , emit: counts_gene_scaled
-    path "*gene_lengths.tsv"             , emit: lengths_gene
-    path "*transcript_tpm.tsv"           , emit: tpm_transcript
-    path "*transcript_counts.tsv"        , emit: counts_transcript
-    path "*transcript_lengths.tsv"       , emit: lengths_transcript
-    path "versions.yml"                  , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
-    prefix = task.ext.prefix ?: "${quant_type}.merged"
-    """
-    tximport.r \\
-        NULL \\
-        quants \\
-        $prefix \\
-        $quant_type \\
-        $tx2gene
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        bioconductor-tximeta: \$(Rscript -e "library(tximeta); cat(as.character(packageVersion('tximeta')))")
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml
new file mode 100644
index 000000000..4c6db6276
--- /dev/null
+++ b/modules/nf-core/bbmap/bbsplit/environment.yml
@@ -0,0 +1,7 @@
+name: bbmap_bbsplit
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bbmap=39.01
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
index f82bb9e47..f308f6983 100644
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -3,7 +3,7 @@ process BBMAP_BBSPLIT {
     label 'process_high'
     label 'error_retry'
 
-    conda "bioconda::bbmap=39.01"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0':
         'biocontainers/bbmap:39.01--h5c4e2a8_0' }"
@@ -12,7 +12,7 @@ process BBMAP_BBSPLIT {
     tuple val(meta), path(reads)
     path  index
     path  primary_ref
-    tuple val(other_ref_names), path (other_ref_paths)
+    tuple val(other_ref_names), path(other_ref_paths)
     val   only_build_index
 
     output:
@@ -20,6 +20,7 @@ process BBMAP_BBSPLIT {
     tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq
     tuple val(meta), path('*fastq.gz')        , optional:true, emit: all_fastq
     tuple val(meta), path('*txt')             , optional:true, emit: stats
+    tuple val(meta), path('*.log')            , optional:true, emit: log
     path "versions.yml"                       , emit: versions
 
     when:
@@ -40,27 +41,19 @@ process BBMAP_BBSPLIT {
     other_ref_names.eachWithIndex { name, index ->
         other_refs << "ref_${name}=${other_ref_paths[index]}"
     }
+
+    def fastq_in=''
+    def fastq_out=''
+    def index_files=''
+    def refstats_cmd=''
+
     if (only_build_index) {
         if (primary_ref && other_ref_names && other_ref_paths) {
-            """
-            bbsplit.sh \\
-                -Xmx${avail_mem}M \\
-                ref_primary=$primary_ref \\
-                ${other_refs.join(' ')} \\
-                path=bbsplit \\
-                threads=$task.cpus \\
-                $args
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
-            END_VERSIONS
-            """
+            index_files = 'ref_primary=' +primary_ref + ' ' + other_refs.join(' ') + ' path=bbsplit'
         } else {
             log.error 'ERROR: Please specify as input a primary fasta file along with names and paths to non-primary fasta files.'
         }
     } else {
-        def index_files = ''
         if (index) {
             index_files = "path=$index"
         } else if (primary_ref && other_ref_names && other_ref_paths) {
@@ -68,22 +61,71 @@ process BBMAP_BBSPLIT {
         } else {
             log.error 'ERROR: Please either specify a BBSplit index as input or a primary fasta file along with names and paths to non-primary fasta files.'
         }
-        def fastq_in  = meta.single_end ? "in=${reads}" : "in=${reads[0]} in2=${reads[1]}"
-        def fastq_out = meta.single_end ? "basename=${prefix}_%.fastq.gz" : "basename=${prefix}_%_#.fastq.gz"
-        """
-        bbsplit.sh \\
-            -Xmx${avail_mem}M \\
-            $index_files \\
-            threads=$task.cpus \\
-            $fastq_in \\
-            $fastq_out \\
-            refstats=${prefix}.stats.txt \\
-            $args
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
-        END_VERSIONS
-        """
+        fastq_in  = meta.single_end ? "in=${reads}" : "in=${reads[0]} in2=${reads[1]}"
+        fastq_out = meta.single_end ? "basename=${prefix}_%.fastq.gz" : "basename=${prefix}_%_#.fastq.gz"
+        refstats_cmd = 'refstats=' + prefix + '.stats.txt'
+    }
+    """
+
+    # When we stage in the index files the time stamps get disturbed, which
+    # bbsplit doesn't like. Fix the time stamps in its summaries. This needs to
+    # be done via Java to match what bbmap does
+
+    if [ $index ]; then
+        for summary_file in \$(find $index/ref/genome -name summary.txt); do
+            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
+            mod=\$(echo "System.out.println(java.nio.file.Files.getLastModifiedTime(java.nio.file.Paths.get(\\"\$src\\")).toMillis());" | jshell -J-Djdk.lang.Process.launchMechanism=vfork -)
+            sed "s|^last modified.*|last modified\\t\$mod|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+        done
+    fi
+
+    # Run BBSplit
+
+    bbsplit.sh \\
+        -Xmx${avail_mem}M \\
+        $index_files \\
+        threads=$task.cpus \\
+        $fastq_in \\
+        $fastq_out \\
+        $refstats_cmd \\
+        $args 2> >(tee ${prefix}.log >&2)
+
+    # Summary files will have an absolute path that will make the index
+    # impossible to use in other processes- we can fix that
+
+    for summary_file in \$(find bbsplit/ref/genome -name summary.txt); do
+        src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
+        sed "s|^source.*|source\\t\$src|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def other_refs = ''
+    other_ref_names.eachWithIndex { name, index ->
+        other_refs += "echo '' | gzip > ${prefix}_${name}.fastq.gz"
     }
+    """
+    if [ ! -d bbsplit ]; then
+        mkdir bbsplit
+    fi
+
+    if ! (${only_build_index}); then
+        echo '' | gzip >  ${prefix}_primary.fastq.gz
+        ${other_refs}
+        touch ${prefix}.stats.txt
+    fi
+
+    touch ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml
index caa3dd66c..f4e0a5ed5 100644
--- a/modules/nf-core/bbmap/bbsplit/meta.yml
+++ b/modules/nf-core/bbmap/bbsplit/meta.yml
@@ -11,9 +11,7 @@ tools:
       description: BBMap is a short read aligner, as well as various other bioinformatic tools.
       homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
       documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
-
       licence: ["UC-LBL license (see package)"]
-
 input:
   - meta:
       type: map
@@ -42,7 +40,6 @@ input:
   - only_build_index:
       type: string
       description: true = only build index; false = mapping
-
 output:
   - meta:
       type: map
@@ -69,7 +66,9 @@ output:
       type: file
       description: Tab-delimited text file containing mapping statistics
       pattern: "*.txt"
-
 authors:
   - "@joseespinosa"
   - "@drpatelh"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
diff --git a/modules/nf-core/bbmap/bbsplit/nextflow.config b/modules/nf-core/bbmap/bbsplit/nextflow.config
new file mode 100644
index 000000000..8d71e9d85
--- /dev/null
+++ b/modules/nf-core/bbmap/bbsplit/nextflow.config
@@ -0,0 +1,20 @@
+if (!params.skip_bbsplit) {
+    process {
+        withName: 'BBMAP_BBSPLIT' {
+            ext.args   = 'build=1 ambiguous2=all maxindel=150000 ow=f'
+            publishDir = [
+                [
+                    path: { "${params.outdir}/bbsplit" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.txt'
+                ],
+                [
+                    path: { params.save_bbsplit_reads ? "${params.outdir}/bbsplit" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.fastq.gz',
+                    saveAs: { params.save_bbsplit_reads ? it : null }
+                ]
+            ]
+        }
+    }
+}
diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
new file mode 100644
index 000000000..0674d247f
--- /dev/null
+++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
@@ -0,0 +1,189 @@
+nextflow_process {
+
+    name "Test Process BBMAP_BBSPLIT"
+    script "../main.nf"
+    process "BBMAP_BBSPLIT"
+
+    test("sarscov2_se_fastq_fasta_chr22_fasta - index") {
+
+        when {
+            process {
+                """
+                input[0] = [[:], []]
+                input[1] = []
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[3] = Channel.of([
+                    [ 'human' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
+                ])
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path("${process.out.index[0]}").exists() },
+                { assert path(process.out.log[0][1]).text.contains("No index available") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2_se_fastq_fasta_chr22_fasta - index - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [[:], []]
+                input[1] = []
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                input[3] = Channel.of([
+                    [ 'human' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
+                ])
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2_se_fastq_fasta_chr22_fasta") {
+
+        setup {
+
+            run("BBMAP_BBSPLIT", alias: "BBMAP_BBSPLIT_INDEX") {
+                script "../main.nf"
+                process {
+                    """
+                    input[0] = [[:], []]
+                    input[1] = []
+                    input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                    input[3] = Channel.of([
+                        [ 'human' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
+                    ])
+                    input[4] = true
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test', single_end:true ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ])
+                    input[1] = BBMAP_BBSPLIT_INDEX.out.index
+                    input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                    input[3] = Channel.of([
+                        [ 'human' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
+                    ])
+                    input[4] = false
+                    """
+                }
+        }
+
+        then {
+            def filesToExclude = [
+                "info.txt",
+                "reflist.txt",
+                "scaffolds.txt.gz",
+                "summary.txt"
+            ]
+
+            def outputFiles = []
+            def outputDirectory = new File(process.out.index[0])
+            outputDirectory.eachFileRecurse { file ->
+                if (file.isFile()){
+                    outputFiles << file
+                    }
+            }
+
+            def filesExist = filesToExclude.every { excludeName ->
+                outputFiles.any { file ->
+                    file.getName().endsWith(excludeName) && file.exists()
+                }
+            }
+
+            def filteredFiles = outputFiles
+                .findAll { file ->
+                    !filesToExclude.any { excludeName ->
+                        file.getName().endsWith(excludeName)
+                    }
+                }.sort{ it.getName()}
+
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.log[0][1]).text.contains("If you wish to regenerate the index") },
+                { assert filesExist : "One or more files to exclude do not exist" },
+                { assert snapshot(
+                    filteredFiles,
+                    process.out.versions
+                ).match()}
+            )
+        }
+    }
+
+    test("sarscov2_se_fastq_fasta_chr22_fasta - stub") {
+
+        options "-stub"
+
+        setup {
+
+            run("BBMAP_BBSPLIT", alias: "BBMAP_BBSPLIT_INDEX") {
+                script "../main.nf"
+                process {
+                    """
+                    input[0] = [[:], []]
+                    input[1] = []
+                    input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                    input[3] = Channel.of([
+                        [ 'human' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
+                    ])
+                    input[4] = true
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                    input[0] = Channel.of([
+                        [ id:'test', single_end:true ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ])
+                    input[1] = BBMAP_BBSPLIT_INDEX.out.index
+                    input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
+                    input[3] = Channel.of([
+                        [ 'human' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
+                    ])
+                    input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap
new file mode 100644
index 000000000..0d648d7d6
--- /dev/null
+++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap
@@ -0,0 +1,199 @@
+{
+    "sarscov2_se_fastq_fasta_chr22_fasta": {
+        "content": [
+            [
+                "chr1.chrom.gz:md5,8fec4c63ec642613ad10adf4cc2e6ade",
+                "chr1_index_k13_c13_b1.block:md5,385913c1e84b77dc7bf36288ee1c8706",
+                "chr1_index_k13_c13_b1.block2.gz:md5,2556b45206835a0ff7078d683b5fd6e2",
+                "merged_ref_9222711925172838098.fa.gz:md5,983cef447fb28394b88a5b49b3579f0c",
+                "namelist.txt:md5,45e7a4cdc7a11a39ada56844ca3a1e30"
+            ],
+            [
+                "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:41:32.116928"
+    },
+    "sarscov2_se_fastq_fasta_chr22_fasta - index": {
+        "content": [
+            [
+                "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:41:06.072212"
+    },
+    "sarscov2_se_fastq_fasta_chr22_fasta - index - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            
+                        },
+                        "null.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+                ],
+                "all_fastq": [
+                    
+                ],
+                "index": [
+                    [
+                        
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            
+                        },
+                        "null.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "primary_fastq": [
+                    
+                ],
+                "stats": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:45:21.48352"
+    },
+    "sarscov2_se_fastq_fasta_chr22_fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+                ],
+                "all_fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "index": [
+                    [
+                        
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "primary_fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:51:38.805111"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml
new file mode 100644
index 000000000..8fbe20c31
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/environment.yml
@@ -0,0 +1,7 @@
+name: bedtools_genomecov
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bedtools=2.31.1
diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf
new file mode 100644
index 000000000..8403c5303
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/main.nf
@@ -0,0 +1,77 @@
+process BEDTOOLS_GENOMECOV {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15':
+        'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }"
+
+    input:
+    tuple val(meta), path(intervals), val(scale)
+    path  sizes
+    val   extension
+    val   sort
+
+    output:
+    tuple val(meta), path("*.${extension}"), emit: genomecov
+    path  "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args  ?: ''
+    def args_list = args.tokenize()
+    args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
+    if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) {
+        args += " -bg"
+    }
+    // Sorts output file by chromosome and position using additional options for performance and consistency
+    // See https://www.biostars.org/p/66927/ for further details
+    def buffer   = task.memory ? "--buffer-size=${task.memory.toGiga().intdiv(2)}G" : ''
+    def sort_cmd = sort ? "| LC_ALL=C sort --parallel=$task.cpus $buffer -k1,1 -k2,2n" : ''
+
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (intervals.name =~ /\.bam/) {
+        """
+        bedtools \\
+            genomecov \\
+            -ibam $intervals \\
+            $args \\
+            $sort_cmd \\
+            > ${prefix}.${extension}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+        END_VERSIONS
+        """
+    } else {
+        """
+        bedtools \\
+            genomecov \\
+            -i $intervals \\
+            -g $sizes \\
+            $args \\
+            $sort_cmd \\
+            > ${prefix}.${extension}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+        END_VERSIONS
+        """
+    }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch  ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml
new file mode 100644
index 000000000..2b2385e3e
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/meta.yml
@@ -0,0 +1,59 @@
+name: bedtools_genomecov
+description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
+keywords:
+  - bed
+  - bam
+  - genomecov
+  - bedtools
+  - histogram
+tools:
+  - bedtools:
+      description: |
+        A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
+      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - intervals:
+      type: file
+      description: BAM/BED/GFF/VCF
+      pattern: "*.{bam|bed|gff|vcf}"
+  - scale:
+      type: integer
+      description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
+  - sizes:
+      type: file
+      description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
+  - extension:
+      type: string
+      description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - genomecov:
+      type: file
+      description: Computed genome coverage file
+      pattern: "*.${extension}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@edmundmiller"
+  - "@sruthipsuresh"
+  - "@drpatelh"
+  - "@sidorov-si"
+  - "@chris-cheshire"
+maintainers:
+  - "@edmundmiller"
+  - "@sruthipsuresh"
+  - "@drpatelh"
+  - "@sidorov-si"
+  - "@chris-cheshire"
diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test b/modules/nf-core/bedtools/genomecov/tests/main.nf.test
new file mode 100644
index 000000000..b8caa1e11
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test
@@ -0,0 +1,169 @@
+nextflow_process {
+    name "Test Process BEDTOOLS_GENOMECOV"
+    script "../main.nf"
+    process "BEDTOOLS_GENOMECOV"
+    config "./nextflow.config"
+
+    test("sarscov2 - no scale") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true),
+                    1
+                ]
+                // sizes
+                input[1] = []
+                // extension
+                input[2] = "txt"
+                input[3] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - dummy sizes") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true),
+                    0.5
+                ]
+                // sizes
+                input[1] = file('dummy_chromosome_sizes')
+                // extension
+                input[2] = 'txt'
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - scale") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true),
+                    0.5
+                ]
+                // sizes
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.sizes", checkIfExists: true)
+                // extension
+                input[2] = 'txt'
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - no scale - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true),
+                    1
+                ]
+                // sizes
+                input[1] = []
+                // extension
+                input[2] = "txt"
+                input[3] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - dummy sizes - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true),
+                    0.5
+                ]
+                // sizes
+                input[1] = file('dummy_chromosome_sizes')
+                // extension
+                input[2] = 'txt'
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - scale - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true),
+                    0.5
+                ]
+                // sizes
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.sizes", checkIfExists: true)
+                // extension
+                input[2] = 'txt'
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap b/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap
new file mode 100644
index 000000000..da6dbe875
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap
@@ -0,0 +1,200 @@
+{
+    "sarscov2 - dummy sizes": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,01291b6e1beab72e046653e709eb0e10"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,01291b6e1beab72e046653e709eb0e10"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:59:33.898146"
+    },
+    "sarscov2 - no scale - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:59:52.483371"
+    },
+    "sarscov2 - scale": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,de3c59c0ea123bcdbbad27bc0a0a601e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,de3c59c0ea123bcdbbad27bc0a0a601e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:59:43.69501"
+    },
+    "sarscov2 - scale - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:00:09.930036"
+    },
+    "sarscov2 - no scale": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,66083198daca6c001d328ba9616e9b53"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,66083198daca6c001d328ba9616e9b53"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:59:25.448817"
+    },
+    "sarscov2 - dummy sizes - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:00:01.086433"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/genomecov/tests/nextflow.config b/modules/nf-core/bedtools/genomecov/tests/nextflow.config
new file mode 100644
index 000000000..bdb74ae5a
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: BEDTOOLS_GENOMECOV {
+        ext.prefix = { "${meta.id}.coverage" }
+    }
+    
+}
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
new file mode 100644
index 000000000..8c69b121f
--- /dev/null
+++ b/modules/nf-core/cat/fastq/environment.yml
@@ -0,0 +1,7 @@
+name: cat_fastq
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::coreutils=8.30
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
index 5021e6fcb..b68e5f911 100644
--- a/modules/nf-core/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -2,7 +2,7 @@ process CAT_FASTQ {
     tag "$meta.id"
     label 'process_single'
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"
@@ -53,9 +53,9 @@ process CAT_FASTQ {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
-        if (readList.size > 1) {
+        if (readList.size >= 1) {
             """
-            touch ${prefix}.merged.fastq.gz
+            echo '' | gzip > ${prefix}.merged.fastq.gz
 
             cat <<-END_VERSIONS > versions.yml
             "${task.process}":
@@ -64,10 +64,10 @@ process CAT_FASTQ {
             """
         }
     } else {
-        if (readList.size > 2) {
+        if (readList.size >= 2) {
             """
-            touch ${prefix}_1.merged.fastq.gz
-            touch ${prefix}_2.merged.fastq.gz
+            echo '' | gzip > ${prefix}_1.merged.fastq.gz
+            echo '' | gzip > ${prefix}_2.merged.fastq.gz
 
             cat <<-END_VERSIONS > versions.yml
             "${task.process}":
@@ -76,5 +76,4 @@ process CAT_FASTQ {
             """
         }
     }
-
 }
diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml
index 8a39e309f..db4ac3c79 100644
--- a/modules/nf-core/cat/fastq/meta.yml
+++ b/modules/nf-core/cat/fastq/meta.yml
@@ -34,7 +34,9 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@joseespinosa"
   - "@drpatelh"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
diff --git a/modules/nf-core/cat/fastq/nextflow.config b/modules/nf-core/cat/fastq/nextflow.config
new file mode 100644
index 000000000..64de2e49c
--- /dev/null
+++ b/modules/nf-core/cat/fastq/nextflow.config
@@ -0,0 +1,9 @@
+process {
+    withName: 'CAT_FASTQ' {
+        publishDir = [
+            path: { params.save_merged_fastq ? "${params.outdir}/fastq" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename.endsWith('.fastq.gz') && params.save_merged_fastq) ? filename : null }
+        ]
+    }
+}
diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test
new file mode 100644
index 000000000..6cc7aad15
--- /dev/null
+++ b/modules/nf-core/cat/fastq/tests/main.nf.test
@@ -0,0 +1,244 @@
+// NOTE The version snaps may not be consistant
+// https://github.com/nf-core/modules/pull/4087#issuecomment-1767948035
+nextflow_process {
+
+    name "Test Process CAT_FASTQ"
+    script "../main.nf"
+    process "CAT_FASTQ"
+
+    test("test_cat_fastq_single_end") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_paired_end") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_single_end_same_name") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_paired_end_same_name") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_single_end_single_file") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_single_end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_paired_end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_single_end_same_name - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_paired_end_same_name - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_single_end_single_file - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap
new file mode 100644
index 000000000..aec119a94
--- /dev/null
+++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap
@@ -0,0 +1,376 @@
+{
+    "test_cat_fastq_single_end": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-17T17:30:39.816981"
+    },
+    "test_cat_fastq_single_end_same_name": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-17T17:32:35.229332"
+    },
+    "test_cat_fastq_single_end_single_file": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-17T17:34:00.058829"
+    },
+    "test_cat_fastq_paired_end_same_name": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22",
+                            "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22",
+                            "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-17T17:33:33.031555"
+    },
+    "test_cat_fastq_single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:07:28.244999"
+    },
+    "test_cat_fastq_paired_end_same_name - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:07:57.070911"
+    },
+    "test_cat_fastq_single_end_same_name - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:07:46.796254"
+    },
+    "test_cat_fastq_paired_end": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22",
+                            "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22",
+                            "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-17T17:32:02.270935"
+    },
+    "test_cat_fastq_paired_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:07:37.807553"
+    },
+    "test_cat_fastq_single_end_single_file - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:14:51.861264"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml
new file mode 100644
index 000000000..e587338b5
--- /dev/null
+++ b/modules/nf-core/custom/catadditionalfasta/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "custom_catadditionalfasta"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::python=3.9.5
diff --git a/modules/nf-core/custom/catadditionalfasta/main.nf b/modules/nf-core/custom/catadditionalfasta/main.nf
new file mode 100644
index 000000000..88ce4954b
--- /dev/null
+++ b/modules/nf-core/custom/catadditionalfasta/main.nf
@@ -0,0 +1,37 @@
+process CUSTOM_CATADDITIONALFASTA {
+    tag "$meta.id"
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'biocontainers/python:3.9--1' }"
+
+    input:
+    tuple val(meta), path(fasta), path(gtf)
+    tuple val(meta2), path(add_fasta)
+    val  biotype
+
+    output:
+    tuple val(meta), path("*/*.fasta") , emit: fasta
+    tuple val(meta), path("*/*.gtf")   , emit: gtf
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'fasta2gtf.py'
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir out
+    touch out/genome_transcriptome.fasta
+    touch out/genome_transcriptome.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | grep -v "Python ")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/custom/catadditionalfasta/meta.yml b/modules/nf-core/custom/catadditionalfasta/meta.yml
new file mode 100644
index 000000000..8a9505d30
--- /dev/null
+++ b/modules/nf-core/custom/catadditionalfasta/meta.yml
@@ -0,0 +1,61 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "custom_catadditionalfasta"
+description: Custom module to Add a new fasta file to an old one and update an associated GTF
+keywords:
+  - fasta
+  - gtf
+  - genomics
+tools:
+  - "custom":
+      description: "Custom module to Add a new fasta file to an old one and update an associated GTF"
+      tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/catadditionalfasta/main.nf"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing fasta information
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing additional fasta information
+  - fasta:
+      type: file
+      description: FASTA-format sequence file
+      pattern: "*.{fasta,fa}"
+  - gtf:
+      type: file
+      description: GTF-format annotation file for fasta
+      pattern: "*.gtf"
+  - add_fasta:
+      type: file
+      description: FASTA-format file of additional sequences
+      pattern: "*.fa"
+  - biotype:
+      type: string
+      description: Biotype to apply to new GTF entries
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing fasta information
+  - fasta:
+      type: file
+      description: FASTA-format combined sequence file
+      pattern: "*.{fasta,fa}"
+  - gtf:
+      type: file
+      description: GTF-format combined annotation file
+      pattern: "*.gtf"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@pinin4fjords"
+maintainers:
+  - "@pinin4fjords"
diff --git a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py
new file mode 100755
index 000000000..194a04160
--- /dev/null
+++ b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py
@@ -0,0 +1,134 @@
+#!/usr/bin/env python3
+
+# Written by Pranathi Vemuri, later modified by Jonathan Manning and released under the MIT license.
+
+import os
+import logging
+import platform
+from typing import Iterator, Tuple
+from itertools import groupby
+
+
+def setup_logging() -> logging.Logger:
+    """Configure logging for the script.
+
+    Returns:
+        logging.Logger: Configured logger instance.
+    """
+    logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
+    logger = logging.getLogger(__file__)
+    logger.setLevel(logging.INFO)
+    return logger
+
+
+def format_yaml_like(data: dict, indent: int = 0) -> str:
+    """Formats a dictionary to a YAML-like string.
+
+    Args:
+        data (dict): The dictionary to format.
+        indent (int): The current indentation level.
+
+    Returns:
+        str: A string formatted as YAML.
+    """
+    yaml_str = ""
+    for key, value in data.items():
+        spaces = "  " * indent
+        if isinstance(value, dict):
+            yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}"
+        else:
+            yaml_str += f"{spaces}{key}: {value}\\n"
+    return yaml_str
+
+
+def parse_fasta(fasta_file: str) -> Iterator[Tuple[str, str]]:
+    """Parse a fasta file and yield tuples of header and sequence.
+
+    Args:
+        fasta_file (str): Path to the fasta file.
+
+    Yields:
+        Iterator[Tuple[str, str]]: Tuples of header and sequence from the fasta file.
+
+
+    modified from Brent Pedersen
+    Correct Way To Parse A Fasta File In Python
+    given a fasta file. yield tuples of header, sequence
+
+    Fasta iterator from https://www.biostars.org/p/710/#120760
+    """
+    with open(fasta_file) as file_handle:
+        fasta_iter = (x[1] for x in groupby(file_handle, lambda line: line[0] == ">"))
+        for header in fasta_iter:
+            header_str = next(header)[1:].strip()
+            sequence = "".join(s.strip() for s in next(fasta_iter))
+            yield (header_str, sequence)
+
+
+def fasta_to_gtf(fasta: str, output_file: str, biotype: str) -> None:
+    """
+    Read a fasta file and create a GTF file.
+
+    Args:
+        fasta (str): Path to the fasta file.
+        output_file (str): Path for the output GTF file.
+        biotype (str): The biotype to use in the GTF.
+    """
+    fasta_iter = parse_fasta(fasta)
+    lines = []
+
+    for header, sequence in fasta_iter:
+        seq_name = header.split()[0].replace(" ", "_")
+        line = generate_gtf_line(seq_name, len(sequence), biotype)
+        lines.append(line)
+
+    with open(output_file, "w") as file_handle:
+        file_handle.writelines(lines)
+
+
+def generate_gtf_line(name: str, length: int, biotype: str) -> str:
+    """Generate a single GTF line given sequence name, length, and biotype.
+
+    Args:
+        name (str): Name of the sequence.
+        length (int): Length of the sequence.
+        biotype (str): Biotype of the sequence.
+
+    Returns:
+        str: A formatted GTF line.
+    """
+    biotype_attr = f' {biotype} "transgene";' if biotype else ""
+    attributes = f'exon_id "{name}.1"; exon_number "1";{biotype_attr} gene_id "{name}_gene"; gene_name "{name}_gene"; gene_source "custom"; transcript_id "{name}_gene"; transcript_name "{name}_gene";\\n'
+    return f"{name}\\ttransgene\\texon\\t1\\t{length}\\t.\\t+\\t.\\t{attributes}"
+
+
+def main() -> None:
+    # Parse arguments using argparse (not shown for brevity)
+    # Example: args = parser.parse_args()
+
+    logger = setup_logging()
+    logger.info("Starting fasta to GTF conversion.")
+
+    # Add fasta lines to GTF
+    add_name = os.path.splitext(os.path.basename("$add_fasta"))[0]
+    fasta_to_gtf("$add_fasta", f"{add_name}.gtf", "$biotype")
+
+    # Concatenate new fasta to existing fasta, and the GTF we just generated to the GTF
+    genome_name = "$params.genome" if "$params.genome" != "null" else os.path.splitext(os.path.basename("$fasta"))[0]
+    output_prefix = "$task.ext.prefix" if "$task.ext.prefix" != "null" else f"{genome_name}_{add_name}"
+
+    os.mkdir("out")
+    os.system(f"cat $fasta $add_fasta > out/{output_prefix}.fasta")
+    os.system(f"cat $gtf {add_name}.gtf > out/{output_prefix}.gtf")
+
+    logger.info("Conversion completed successfully.")
+
+    # Write the versions
+    versions_this_module = {}
+    versions_this_module["${task.process}"] = {"python": platform.python_version()}
+    with open("versions.yml", "w") as f:
+        f.write(format_yaml_like(versions_this_module))
+
+
+if __name__ == "__main__":
+    main()
diff --git a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test
new file mode 100644
index 000000000..878c05d16
--- /dev/null
+++ b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test
@@ -0,0 +1,69 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_CATADDITIONALFASTA"
+    script "../main.nf"
+    process "CUSTOM_CATADDITIONALFASTA"
+
+    test("sarscov2 - fastq - gtf") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
+                ])
+                input[2] = 'test_biotype'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.fasta,
+                    process.out.gtf,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - fastq - gtf - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
+                ])
+                input[2] = 'test_biotype'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap
new file mode 100644
index 000000000..4767fd9a0
--- /dev/null
+++ b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap
@@ -0,0 +1,85 @@
+{
+    "sarscov2 - fastq - gtf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "genome_transcriptome.fasta:md5,6a20c1a2e465519320a0d01f338f5cb5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "genome_transcriptome.gtf:md5,bc88d95e7f27540e6b9906105d5be361"
+                ]
+            ],
+            [
+                "versions.yml:md5,26f47339777a265af57338ac7f0f8798"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:19:28.965471"
+    },
+    "sarscov2 - fastq - gtf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,451e5a1afee71b2b916b6f2ccc47e508"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,451e5a1afee71b2b916b6f2ccc47e508"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:19:38.549677"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
deleted file mode 100644
index 2ec89807d..000000000
--- a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/custom/dumpsoftwareversions'
---- modules/nf-core/custom/dumpsoftwareversions/main.nf
-+++ modules/nf-core/custom/dumpsoftwareversions/main.nf
-@@ -2,10 +2,10 @@
-     label 'process_single'
- 
-     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
--    conda "${moduleDir}/environment.yml"
-+    conda "bioconda::multiqc=1.19"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' :
--        'biocontainers/multiqc:1.17--pyhdfd78af_0' }"
-+        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
-+        'biocontainers/multiqc:1.19--pyhdfd78af_0' }"
- 
-     input:
-     path versions
-
-************************************************************
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
deleted file mode 100644
index b2dcf480e..000000000
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_single'
-
-    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.19"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.19--pyhdfd78af_0' }"
-
-    input:
-    path versions
-
-    output:
-    path "software_versions.yml"    , emit: yml
-    path "software_versions_mqc.yml", emit: mqc_yml
-    path "versions.yml"             , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    template 'dumpsoftwareversions.py'
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
deleted file mode 100644
index 5f15a5fde..000000000
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: custom_dumpsoftwareversions
-description: Custom module used to dump software versions within the nf-core pipeline template
-keywords:
-  - custom
-  - dump
-  - version
-tools:
-  - custom:
-      description: Custom module used to dump software versions within the nf-core pipeline template
-      homepage: https://github.com/nf-core/tools
-      documentation: https://github.com/nf-core/tools
-      licence: ["MIT"]
-input:
-  - versions:
-      type: file
-      description: YML file containing software versions
-      pattern: "*.yml"
-output:
-  - yml:
-      type: file
-      description: Standard YML file containing software versions
-      pattern: "software_versions.yml"
-  - mqc_yml:
-      type: file
-      description: MultiQC custom content YML file containing software versions
-      pattern: "software_versions_mqc.yml"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@drpatelh"
-  - "@grst"
-maintainers:
-  - "@drpatelh"
-  - "@grst"
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
deleted file mode 100755
index da0334085..000000000
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ /dev/null
@@ -1,101 +0,0 @@
-#!/usr/bin/env python
-
-
-"""Provide functions to merge multiple versions.yml files."""
-
-
-import yaml
-import platform
-from textwrap import dedent
-
-
-def _make_versions_html(versions):
-    """Generate a tabular HTML output of all versions for MultiQC."""
-    html = [
-        dedent(
-            """\\
-            <style>
-            #nf-core-versions tbody:nth-child(even) {
-                background-color: #f2f2f2;
-            }
-            </style>
-            <table class="table" style="width:100%" id="nf-core-versions">
-                <thead>
-                    <tr>
-                        <th> Process Name </th>
-                        <th> Software </th>
-                        <th> Version  </th>
-                    </tr>
-                </thead>
-            """
-        )
-    ]
-    for process, tmp_versions in sorted(versions.items()):
-        html.append("<tbody>")
-        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
-            html.append(
-                dedent(
-                    f"""\\
-                    <tr>
-                        <td><samp>{process if (i == 0) else ''}</samp></td>
-                        <td><samp>{tool}</samp></td>
-                        <td><samp>{version}</samp></td>
-                    </tr>
-                    """
-                )
-            )
-        html.append("</tbody>")
-    html.append("</table>")
-    return "\\n".join(html)
-
-
-def main():
-    """Load all version files and generate merged output."""
-    versions_this_module = {}
-    versions_this_module["${task.process}"] = {
-        "python": platform.python_version(),
-        "yaml": yaml.__version__,
-    }
-
-    with open("$versions") as f:
-        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-    # aggregate versions by the module name (derived from fully-qualified process name)
-    versions_by_module = {}
-    for process, process_versions in versions_by_process.items():
-        module = process.split(":")[-1]
-        try:
-            if versions_by_module[module] != process_versions:
-                raise AssertionError(
-                    "We assume that software versions are the same between all modules. "
-                    "If you see this error-message it means you discovered an edge-case "
-                    "and should open an issue in nf-core/tools. "
-                )
-        except KeyError:
-            versions_by_module[module] = process_versions
-
-    versions_by_module["Workflow"] = {
-        "Nextflow": "$workflow.nextflow.version",
-        "$workflow.manifest.name": "$workflow.manifest.version",
-    }
-
-    versions_mqc = {
-        "id": "software_versions",
-        "section_name": "${workflow.manifest.name} Software Versions",
-        "section_href": "https://github.com/${workflow.manifest.name}",
-        "plot_type": "html",
-        "description": "are collected at run time from the software output.",
-        "data": _make_versions_html(versions_by_module),
-    }
-
-    with open("software_versions.yml", "w") as f:
-        yaml.dump(versions_by_module, f, default_flow_style=False)
-    with open("software_versions_mqc.yml", "w") as f:
-        yaml.dump(versions_mqc, f, default_flow_style=False)
-
-    with open("versions.yml", "w") as f:
-        yaml.dump(versions_this_module, f, default_flow_style=False)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
deleted file mode 100644
index eec1db10a..000000000
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
+++ /dev/null
@@ -1,38 +0,0 @@
-nextflow_process {
-
-    name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS"
-    script "../main.nf"
-    process "CUSTOM_DUMPSOFTWAREVERSIONS"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "custom"
-    tag "dumpsoftwareversions"
-    tag "custom/dumpsoftwareversions"
-
-    test("Should run without failures") {
-        when {
-            process {
-                """
-                def tool1_version = '''
-                TOOL1:
-                    tool1: 0.11.9
-                '''.stripIndent()
-
-                def tool2_version = '''
-                TOOL2:
-                    tool2: 1.9
-                '''.stripIndent()
-
-                input[0] = Channel.of(tool1_version, tool2_version).collectFile()
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
deleted file mode 100644
index 4274ed57a..000000000
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
+++ /dev/null
@@ -1,27 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    "software_versions.yml:md5,1c851188476409cda5752ce971b20b58"
-                ],
-                "1": [
-                    "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d"
-                ],
-                "2": [
-                    "versions.yml:md5,3843ac526e762117eedf8825b40683df"
-                ],
-                "mqc_yml": [
-                    "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d"
-                ],
-                "versions": [
-                    "versions.yml:md5,3843ac526e762117eedf8825b40683df"
-                ],
-                "yml": [
-                    "software_versions.yml:md5,1c851188476409cda5752ce971b20b58"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-03T14:43:22.157011"
-    }
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
deleted file mode 100644
index 405aa24ae..000000000
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-custom/dumpsoftwareversions:
-  - modules/nf-core/custom/dumpsoftwareversions/**
diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml
new file mode 100644
index 000000000..2ecd0128f
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/environment.yml
@@ -0,0 +1,8 @@
+name: custom_getchromsizes
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
index 060a2e885..3edf7c221 100644
--- a/modules/nf-core/custom/getchromsizes/main.nf
+++ b/modules/nf-core/custom/getchromsizes/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
     tag "$fasta"
     label 'process_single'
 
-    conda "bioconda::samtools=1.16.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'biocontainers/samtools:1.16.1--h6899075_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -35,6 +35,9 @@ process CUSTOM_GETCHROMSIZES {
     """
     touch ${fasta}.fai
     touch ${fasta}.sizes
+    if [[ "${fasta.extension}" == "gz" ]]; then
+        touch ${fasta}.gzi
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/custom/getchromsizes/meta.yml b/modules/nf-core/custom/getchromsizes/meta.yml
index 219ca1d8e..529be07e4 100644
--- a/modules/nf-core/custom/getchromsizes/meta.yml
+++ b/modules/nf-core/custom/getchromsizes/meta.yml
@@ -12,7 +12,6 @@ tools:
       tool_dev_url: https://github.com/samtools/samtools
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
-
 input:
   - meta:
       type: map
@@ -23,7 +22,6 @@ input:
       type: file
       description: FASTA file
       pattern: "*.{fa,fasta,fna,fas}"
-
 output:
   - meta:
       type: map
@@ -46,8 +44,11 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@tamara-hodgetts"
   - "@chris-cheshire"
   - "@muffato"
+maintainers:
+  - "@tamara-hodgetts"
+  - "@chris-cheshire"
+  - "@muffato"
diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test b/modules/nf-core/custom/getchromsizes/tests/main.nf.test
new file mode 100644
index 000000000..2dadc1a55
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test
@@ -0,0 +1,94 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_GETCHROMSIZES"
+    script "../main.nf"
+    process "CUSTOM_GETCHROMSIZES"
+
+    test("test_custom_getchromsizes") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_custom_getchromsizes_bgzip") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_custom_getchromsizes - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_custom_getchromsizes_bgzip - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap
new file mode 100644
index 000000000..c37b284d7
--- /dev/null
+++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap
@@ -0,0 +1,242 @@
+{
+    "test_custom_getchromsizes_bgzip - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:38:36.927106"
+    },
+    "test_custom_getchromsizes": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T13:22:34.14237"
+    },
+    "test_custom_getchromsizes_bgzip": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T13:23:06.241379"
+    },
+    "test_custom_getchromsizes - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:24:05.697845"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml
new file mode 100644
index 000000000..a859dc881
--- /dev/null
+++ b/modules/nf-core/custom/tx2gene/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "custom_tx2gene"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python=3.9.5
diff --git a/modules/nf-core/custom/tx2gene/main.nf b/modules/nf-core/custom/tx2gene/main.nf
new file mode 100644
index 000000000..99c00aa06
--- /dev/null
+++ b/modules/nf-core/custom/tx2gene/main.nf
@@ -0,0 +1,36 @@
+process CUSTOM_TX2GENE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'biocontainers/python:3.9--1' }"
+
+    input:
+    tuple val(meta), path(gtf)
+    tuple val(meta2), path ("quants/*")
+    val quant_type
+    val id
+    val extra
+
+    output:
+    tuple val(meta), path("*tx2gene.tsv"), emit: tx2gene
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'tx2gene.py'
+
+    stub:
+    """
+    touch ${meta.id}.tx2gene.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/custom/tx2gene/meta.yml b/modules/nf-core/custom/tx2gene/meta.yml
new file mode 100644
index 000000000..d991bf1be
--- /dev/null
+++ b/modules/nf-core/custom/tx2gene/meta.yml
@@ -0,0 +1,65 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "custom_tx2gene"
+description: Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications.
+keywords:
+  - gene
+  - gtf
+  - pseudoalignment
+  - transcript
+tools:
+  - "custom":
+      description: |
+        "Custom module to create a transcript to gene mapping from a GTF and
+        check it against transcript quantifications"
+      tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information related to the GTF file
+        e.g. `[ id:'yeast' ]`
+  - gtf:
+      type: file
+      description: An annotation file of the reference genome in GTF format
+      pattern: "*.gtf"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole
+        e.g. `[ id:'SRP123456' ]`
+  - quants:
+      type: directory
+      description: Paths to subdirectories corresponding to
+        sample-wise runs of Salmon or Kallisto
+  - quant_type:
+      type: string
+      description: Quantification type, 'kallisto' or 'salmon'
+  - id:
+      type: string
+      description: Gene ID attribute in the GTF file (default= gene_id)
+  - extra:
+      type: string
+      description: Extra gene attribute in the GTF file (default= gene_name)
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information related to the GTF file
+        e.g. `[ id:'yeast' ]`
+  - tx2gene:
+      type: file
+      description: A transcript/ gene mapping table in TSV format
+      pattern: "*.tx2gene.tsv"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@pinin4fjords"
+maintainers:
+  - "@pinin4fjords"
diff --git a/bin/tx2gene.py b/modules/nf-core/custom/tx2gene/templates/tx2gene.py
similarity index 75%
rename from bin/tx2gene.py
rename to modules/nf-core/custom/tx2gene/templates/tx2gene.py
index d8256f5f9..8c2e3b1f4 100755
--- a/bin/tx2gene.py
+++ b/modules/nf-core/custom/tx2gene/templates/tx2gene.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # Written by Lorena Pantano with subsequent reworking by Jonathan Manning. Released under the MIT license.
 
@@ -6,6 +6,7 @@
 import argparse
 import glob
 import os
+import platform
 import re
 from collections import Counter, defaultdict, OrderedDict
 from collections.abc import Set
@@ -17,6 +18,26 @@
 logger.setLevel(logging.INFO)
 
 
+def format_yaml_like(data: dict, indent: int = 0) -> str:
+    """Formats a dictionary to a YAML-like string.
+
+    Args:
+        data (dict): The dictionary to format.
+        indent (int): The current indentation level.
+
+    Returns:
+        str: A string formatted as YAML.
+    """
+    yaml_str = ""
+    for key, value in data.items():
+        spaces = "  " * indent
+        if isinstance(value, dict):
+            yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}"
+        else:
+            yaml_str += f"{spaces}{key}: {value}\\n"
+    return yaml_str
+
+
 def read_top_transcripts(quant_dir: str, file_pattern: str) -> Set[str]:
     """
     Read the top 100 transcripts from the quantification file.
@@ -56,18 +77,17 @@ def discover_transcript_attribute(gtf_file: str, transcripts: Set[str]) -> str:
     with open(gtf_file) as inh:
         # Read GTF file, skipping header lines
         for line in filter(lambda x: not x.startswith("#"), inh):
-            cols = line.split("\t")
+            cols = line.split("\\t")
 
             # Use regular expression to correctly split the attributes string
             attributes_str = cols[8]
-            attributes = dict(re.findall(r'(\S+) "(.*?)(?<!\\)";', attributes_str))
+            attributes = dict(re.findall(r'(\\S+) "(.*?)(?<!\\\\)";', attributes_str))
 
             votes.update(key for key, value in attributes.items() if value in transcripts)
 
     if not votes:
-        # Log a warning if no matching attribute is found
-        logger.warning("No attribute in GTF matching transcripts")
-        return ""
+        # Error out if no matching attribute is found
+        logger.error("No attribute in GTF matching transcripts")
 
     # Check if 'transcript_id' is among the attributes with the highest votes
     if "transcript_id" in votes and votes["transcript_id"] == max(votes.values()):
@@ -105,7 +125,12 @@ def parse_attributes(attributes_text: str) -> Dict[str, str]:
 
 
 def map_transcripts_to_gene(
-    quant_type: str, gtf_file: str, quant_dir: str, gene_id: str, extra_id_field: str, output_file: str
+    quant_type: str,
+    gtf_file: str,
+    quant_dir: str,
+    gene_id: str,
+    extra_id_field: str,
+    output_file: str,
 ) -> bool:
     """
     Map transcripts to gene names and write the output to a file.
@@ -126,28 +151,28 @@ def map_transcripts_to_gene(
     # Discover the attribute that corresponds to transcripts in the GTF
     transcript_attribute = discover_transcript_attribute(gtf_file, transcripts)
 
-    if not transcript_attribute:
-        # If no attribute is found, return False
-        return False
-
     # Open GTF and output file to write the mappings
     # Initialize the set to track seen combinations
     seen = set()
 
     with open(gtf_file) as inh, open(output_file, "w") as output_handle:
+        output_handle.write(f"{transcript_attribute}\\t{gene_id}\\t{extra_id_field}\\n")
         # Parse each line of the GTF, mapping transcripts to genes
         for line in filter(lambda x: not x.startswith("#"), inh):
-            cols = line.split("\t")
+            cols = line.split("\\t")
             attr_dict = parse_attributes(cols[8])
             if gene_id in attr_dict and transcript_attribute in attr_dict:
                 # Create a unique identifier for the transcript-gene combination
-                transcript_gene_pair = (attr_dict[transcript_attribute], attr_dict[gene_id])
+                transcript_gene_pair = (
+                    attr_dict[transcript_attribute],
+                    attr_dict[gene_id],
+                )
 
                 # Check if the combination has already been seen
                 if transcript_gene_pair not in seen:
                     # If it's a new combination, write it to the output and add to the seen set
                     extra_id = attr_dict.get(extra_id_field, attr_dict[gene_id])
-                    output_handle.write(f"{attr_dict[transcript_attribute]}\t{attr_dict[gene_id]}\t{extra_id}\n")
+                    output_handle.write(f"{attr_dict[transcript_attribute]}\\t{attr_dict[gene_id]}\\t{extra_id}\\n")
                     seen.add(transcript_gene_pair)
 
     return True
@@ -155,14 +180,18 @@ def map_transcripts_to_gene(
 
 # Main function to parse arguments and call the mapping function
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Map transcripts to gene names for tximport.")
-    parser.add_argument("--quant_type", type=str, help="Quantification type", default="salmon")
-    parser.add_argument("--gtf", type=str, help="GTF file", required=True)
-    parser.add_argument("--quants", type=str, help="Output of quantification", required=True)
-    parser.add_argument("--id", type=str, help="Gene ID in the GTF file", required=True)
-    parser.add_argument("--extra", type=str, help="Extra ID in the GTF file")
-    parser.add_argument("-o", "--output", dest="output", default="tx2gene.tsv", type=str, help="File with output")
-
-    args = parser.parse_args()
-    if not map_transcripts_to_gene(args.quant_type, args.gtf, args.quants, args.id, args.extra, args.output):
+    if "${task.ext.prefix}" != "null":
+        prefix = "${task.ext.prefix}."
+    elif "$meta.id" != "null":
+        prefix = "${meta.id}."
+    else:
+        prefix = ""
+
+    if not map_transcripts_to_gene("$quant_type", "$gtf", "quants", "$id", "$extra", f"{prefix}tx2gene.tsv"):
         logger.error("Failed to map transcripts to genes.")
+
+    # Write the versions
+    versions_this_module = {}
+    versions_this_module["${task.process}"] = {"python": platform.python_version()}
+    with open("versions.yml", "w") as f:
+        f.write(format_yaml_like(versions_this_module))
diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test
new file mode 100644
index 000000000..e56a0b8fe
--- /dev/null
+++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test
@@ -0,0 +1,86 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_TX2GENE"
+    script "../main.nf"
+    process "CUSTOM_TX2GENE"
+
+    test("saccharomyces_cerevisiae - gtf") {
+
+        setup {
+            run("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test'], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true)
+                ])
+                input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[2] = 'kallisto'
+                input[3] = 'gene_id'
+                input[4] = 'gene_name'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("saccharomyces_cerevisiae - gtf - stub") {
+
+        options "-stub"
+
+        setup {
+            run("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test'], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true)
+                ])
+                input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[2] = 'kallisto'
+                input[3] = 'gene_id'
+                input[4] = 'gene_name'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap
new file mode 100644
index 000000000..c19f10f71
--- /dev/null
+++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "saccharomyces_cerevisiae - gtf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50"
+                ],
+                "tx2gene": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T13:13:11.305047"
+    },
+    "saccharomyces_cerevisiae - gtf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60"
+                ],
+                "tx2gene": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-10T15:15:34.064489"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml
new file mode 100644
index 000000000..58b2bf11d
--- /dev/null
+++ b/modules/nf-core/dupradar/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "dupradar"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::bioconductor-dupradar=1.32.0"
diff --git a/modules/nf-core/dupradar/main.nf b/modules/nf-core/dupradar/main.nf
new file mode 100644
index 000000000..8f3665a67
--- /dev/null
+++ b/modules/nf-core/dupradar/main.nf
@@ -0,0 +1,46 @@
+process DUPRADAR {
+    tag "$meta.id"
+    label 'process_long'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bioconductor-dupradar:1.32.0--r43hdfd78af_0' :
+        'biocontainers/bioconductor-dupradar:1.32.0--r43hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+    tuple val(meta2), path(gtf)
+
+    output:
+    tuple val(meta), path("*_duprateExpDens.pdf")   , emit: scatter2d
+    tuple val(meta), path("*_duprateExpBoxplot.pdf"), emit: boxplot
+    tuple val(meta), path("*_expressionHist.pdf")   , emit: hist
+    tuple val(meta), path("*_dupMatrix.txt")        , emit: dupmatrix
+    tuple val(meta), path("*_intercept_slope.txt")  , emit: intercept_slope
+    tuple val(meta), path("*_mqc.txt")              , emit: multiqc
+    tuple val(meta), path("*.R_sessionInfo.log")    , emit: session_info
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'dupradar.r'
+
+    stub:
+    """
+    touch ${meta.id}_duprateExpDens.pdf
+    touch ${meta.id}_duprateExpBoxplot.pdf
+    touch ${meta.id}_expressionHist.pdf
+    touch ${meta.id}_dupMatrix.txt
+    touch ${meta.id}_intercept_slope.txt
+    touch ${meta.id}_dup_intercept_mqc.txt
+    touch ${meta.id}_duprateExpDensCurve_mqc.txt
+    touch ${meta.id}.R_sessionInfo.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bioconductor-dupradar: \$(Rscript -e "library(dupRadar); cat(as.character(packageVersion('dupRadar')))")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/dupradar/meta.yml b/modules/nf-core/dupradar/meta.yml
new file mode 100644
index 000000000..95960ae98
--- /dev/null
+++ b/modules/nf-core/dupradar/meta.yml
@@ -0,0 +1,85 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "dupradar"
+description: Assessment of duplication rates in RNA-Seq datasets
+keywords:
+  - rnaseq
+  - duplication
+  - genomics
+tools:
+  - "dupradar":
+      description: "Assessment of duplication rates in RNA-Seq datasets"
+      homepage: "https://bioconductor.org/packages/release/bioc/html/dupRadar.html"
+      documentation: "https://bioconductor.org/packages/release/bioc/vignettes/dupRadar/inst/doc/dupRadar.html"
+      tool_dev_url: "https://github.com/ssayols/dupRadar"
+      doi: "10.1186/s12859-016-1276-2"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/SAM file containing read alignments
+      pattern: "*.{bam}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'human' ]
+  - gtf:
+      type: file
+      description: Genomic features annotation in GTF or SAF
+      pattern: "*.{gtf}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - scatter2d:
+      type: file
+      description: PDF duplication rate against total read count plot
+      pattern: "*_duprateExpDens.pdf"
+  - boxplot:
+      type: file
+      description: |
+        PDF duplication rate ~ total reads per kilobase (RPK) boxplot
+      pattern: "*_duprateExpBoxplot.pdf"
+  - hist:
+      type: file
+      description: |
+        PDF expression histogram
+      pattern: "*.pdf"
+  - dupmatrix:
+      type: file
+      description: |
+        Text file containing tags falling on the features described in the GTF
+        file
+      pattern: "*_dupMatrix.txt"
+  - intercept_slope:
+      type: file
+      description: |
+        Text file containing intercept and slope from dupRadar modelling
+      pattern: "*_intercept_slope.txt"
+  - multiqc:
+      type: file
+      description: |
+        dupRadar files for passing to MultiQC
+      pattern: "*_multiqc.txt"
+  - session_info:
+      type: file
+      description: dump of R SessionInfo
+      pattern: "*.log"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@pinin4fjords"
+maintainers:
+  - "@pinin4fjords"
diff --git a/modules/nf-core/dupradar/nextflow.config b/modules/nf-core/dupradar/nextflow.config
new file mode 100644
index 000000000..3ade56ad5
--- /dev/null
+++ b/modules/nf-core/dupradar/nextflow.config
@@ -0,0 +1,35 @@
+if (!params.skip_alignment && !params.skip_qc) {
+    if (!params.skip_dupradar) {
+        process {
+            withName: 'DUPRADAR' {
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/dupradar/scatter_plot" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*Dens.pdf"
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/dupradar/box_plot" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*Boxplot.pdf"
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/dupradar/histogram" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*Hist.pdf"
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/dupradar/gene_data" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*Matrix.txt"
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/dupradar/intercepts_slope" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*slope.txt"
+                    ]
+                ]
+            }
+        }
+    }
+}
diff --git a/modules/nf-core/dupradar/templates/dupradar.r b/modules/nf-core/dupradar/templates/dupradar.r
new file mode 100755
index 000000000..7653e5873
--- /dev/null
+++ b/modules/nf-core/dupradar/templates/dupradar.r
@@ -0,0 +1,187 @@
+#!/usr/bin/env Rscript
+
+# Written by Phil Ewels and released under the MIT license.
+# Ported to nf-core/modules with template by Jonathan Manning
+
+#' Parse out options from a string without recourse to optparse
+#'
+#' @param x Long-form argument list like --opt1 val1 --opt2 val2
+#'
+#' @return named list of options and values similar to optparse
+
+parse_args <- function(x){
+    args_list <- unlist(strsplit(x, ' ?--')[[1]])[-1]
+    args_vals <- lapply(args_list, function(x) scan(text=x, what='character', quiet = TRUE))
+
+    # Ensure the option vectors are length 2 (key/ value) to catch empty ones
+    args_vals <- lapply(args_vals, function(z){ length(z) <- 2; z})
+
+    parsed_args <- structure(lapply(args_vals, function(x) x[2]), names = lapply(args_vals, function(x) x[1]))
+    parsed_args[! is.na(parsed_args)]
+}
+
+################################################
+################################################
+## Pull in module inputs                      ##
+################################################
+################################################
+
+input_bam <- '$bam'
+output_prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix')
+annotation_gtf <- '$gtf'
+threads <- $task.cpus
+args_opt <- parse_args('$task.ext.args')
+feature_type <- ifelse('feature_type' %in% names(args_opt), args_opt[['feature_type']], 'exon')
+
+stranded <- 0
+if ('${meta.strandedness}' == 'forward') {
+    stranded <- 1
+} else if ('${meta.strandedness}' == 'reverse') {
+    stranded <- 2
+}
+
+paired_end <- TRUE
+if ('${meta.single_end}' == 'true'){
+    paired_end <- FALSE
+}
+
+# Debug messages (stderr)
+message("Input bam      : ", input_bam)
+message("Input gtf      : ", annotation_gtf)
+message("Strandness     : ", c("unstranded", "forward", "reverse")[stranded+1])
+message("paired/single  : ", ifelse(paired_end, 'paired', 'single'))
+message("feature type   : ", ifelse(paired_end, 'paired', 'single'))
+message("Nb threads     : ", threads)
+message("Output basename: ", output_prefix)
+
+# Load / install packages
+library("dupRadar")
+library("parallel")
+
+# Duplicate stats
+dm <- analyzeDuprates(input_bam, annotation_gtf, stranded, paired_end, threads, GTF.featureType = feature_type, verbose = TRUE)
+write.table(dm, file=paste(output_prefix, "_dupMatrix.txt", sep=""), quote=F, row.name=F, sep="\t")
+
+# 2D density scatter plot
+pdf(paste0(output_prefix, "_duprateExpDens.pdf"))
+duprateExpDensPlot(DupMat=dm)
+title("Density scatter plot")
+mtext(output_prefix, side=3)
+dev.off()
+fit <- duprateExpFit(DupMat=dm)
+cat(
+    paste("- dupRadar Int (duprate at low read counts):", fit\$intercept),
+    paste("- dupRadar Sl (progression of the duplication rate):", fit\$slope),
+    fill=TRUE, labels=output_prefix,
+    file=paste0(output_prefix, "_intercept_slope.txt"), append=FALSE
+)
+
+# Create a multiqc file dupInt
+sample_name <- gsub("Aligned.sortedByCoord.out.markDups", "", output_prefix)
+line="#id: DupInt
+#plot_type: 'generalstats'
+#pconfig:
+#    dupRadar_intercept:
+#        title: 'dupInt'
+#        namespace: 'DupRadar'
+#        description: 'Intercept value from DupRadar'
+#        max: 100
+#        min: 0
+#        scale: 'RdYlGn-rev'
+Sample dupRadar_intercept"
+
+write(line,file=paste0(output_prefix, "_dup_intercept_mqc.txt"),append=TRUE)
+write(paste(sample_name, fit\$intercept),file=paste0(output_prefix, "_dup_intercept_mqc.txt"),append=TRUE)
+
+# Get numbers from dupRadar GLM
+curve_x <- sort(log10(dm\$RPK))
+curve_y = 100*predict(fit\$glm, data.frame(x=curve_x), type="response")
+# Remove all of the infinite values
+infs = which(curve_x %in% c(-Inf,Inf))
+curve_x = curve_x[-infs]
+curve_y = curve_y[-infs]
+# Reduce number of data points
+curve_x <- curve_x[seq(1, length(curve_x), 10)]
+curve_y <- curve_y[seq(1, length(curve_y), 10)]
+# Convert x values back to real counts
+curve_x = 10^curve_x
+# Write to file
+line="#id: dupradar
+#plot_type: 'linegraph'
+#section_name: 'DupRadar'
+#section_href: 'bioconductor.org/packages/release/bioc/html/dupRadar.html'
+#description: \"provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication.
+#    This plot shows the general linear models - a summary of the gene duplication distributions. \"
+#pconfig:
+#    title: 'DupRadar General Linear Model'
+#    xlog: True
+#    xlab: 'expression (reads/kbp)'
+#    ylab: '% duplicate reads'
+#    ymax: 100
+#    ymin: 0
+#    tt_label: '<b>{point.x:.1f} reads/kbp</b>: {point.y:,.2f}% duplicates'
+#    x_lines:
+#        - color: 'green'
+#          dash: 'LongDash'
+#          label:
+#                text: '0.5 RPKM'
+#          value: 0.5
+#          width: 1
+#        - color: 'red'
+#          dash: 'LongDash'
+#          label:
+#                text: '1 read/bp'
+#          value: 1000
+#          width: 1"
+
+write(line,file=paste0(output_prefix, "_duprateExpDensCurve_mqc.txt"),append=TRUE)
+write.table(
+    cbind(curve_x, curve_y),
+    file=paste0(output_prefix, "_duprateExpDensCurve_mqc.txt"),
+    quote=FALSE, row.names=FALSE, col.names=FALSE, append=TRUE,
+)
+
+# Distribution of expression box plot
+pdf(paste0(output_prefix, "_duprateExpBoxplot.pdf"))
+duprateExpBoxplot(DupMat=dm)
+title("Percent Duplication by Expression")
+mtext(output_prefix, side=3)
+dev.off()
+
+# Distribution of RPK values per gene
+pdf(paste0(output_prefix, "_expressionHist.pdf"))
+expressionHist(DupMat=dm)
+title("Distribution of RPK values per gene")
+mtext(output_prefix, side=3)
+dev.off()
+
+################################################
+################################################
+## R SESSION INFO                             ##
+################################################
+################################################
+
+sink(paste(output_prefix, "R_sessionInfo.log", sep = '.'))
+print(sessionInfo())
+sink()
+
+################################################
+################################################
+## VERSIONS FILE                              ##
+################################################
+################################################
+
+r.version <- strsplit(version[['version.string']], ' ')[[1]][3]
+dupradar.version <- as.character(packageVersion('dupRadar'))
+
+writeLines(
+    c(
+        '"${task.process}":',
+        paste('    bioconductor-dupradar:', dupradar.version)
+    ),
+'versions.yml')
+
+################################################
+################################################
+################################################
+################################################
diff --git a/modules/nf-core/dupradar/tests/main.nf.test b/modules/nf-core/dupradar/tests/main.nf.test
new file mode 100644
index 000000000..60f8dfb7d
--- /dev/null
+++ b/modules/nf-core/dupradar/tests/main.nf.test
@@ -0,0 +1,134 @@
+nextflow_process {
+
+    name "Test Process DUPRADAR"
+    script "../main.nf"
+    process "DUPRADAR"
+
+    test("sarscov2 - bam - single_end") {
+
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true, strandedness:'forward' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.boxplot[0][1]).name,
+                    file(process.out.hist[0][1]).name,
+                    file(process.out.scatter2d[0][1]).name,
+                    process.out.dupmatrix,
+                    process.out.intercept_slopt,
+                    process.out.multiqc,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - single_end - stub") {
+
+        config './nextflow.config'
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true, strandedness:'forward' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - paired_end") {
+
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false, strandedness:'forward' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.boxplot[0][1]).name,
+                    file(process.out.hist[0][1]).name,
+                    file(process.out.scatter2d[0][1]).name,
+                    process.out.dupmatrix,
+                    process.out.intercept_slopt,
+                    process.out.multiqc,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - paired_end - stub") {
+
+        config './nextflow.config'
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false, strandedness:'forward' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'sarscov2' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/dupradar/tests/main.nf.test.snap b/modules/nf-core/dupradar/tests/main.nf.test.snap
new file mode 100644
index 000000000..dc7aba4a5
--- /dev/null
+++ b/modules/nf-core/dupradar/tests/main.nf.test.snap
@@ -0,0 +1,406 @@
+{
+    "sarscov2 - bam - single_end": {
+        "content": [
+            "test_duprateExpBoxplot.pdf",
+            "test_expressionHist.pdf",
+            "test_duprateExpDens.pdf",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true,
+                        "strandedness": "forward"
+                    },
+                    "test_dupMatrix.txt:md5,2beda4c140548a2b8c91bf6bde01ddc6"
+                ]
+            ],
+            null,
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true,
+                        "strandedness": "forward"
+                    },
+                    [
+                        "test_dup_intercept_mqc.txt:md5,11961f0962ffc70e42aa57a12984e0fc",
+                        "test_duprateExpDensCurve_mqc.txt:md5,f7d3432ef52047336b156446281aa6ac"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,cd524e9e74304c2930cf28e2d741d351"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-11T11:21:44.31238184"
+    },
+    "sarscov2 - bam - single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_duprateExpDens.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_duprateExpBoxplot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_expressionHist.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_dupMatrix.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_intercept_slope.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        [
+                            "test_dup_intercept_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_duprateExpDensCurve_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    "versions.yml:md5,cd524e9e74304c2930cf28e2d741d351"
+                ],
+                "boxplot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_duprateExpBoxplot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "dupmatrix": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_dupMatrix.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "hist": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_expressionHist.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "intercept_slope": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_intercept_slope.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        [
+                            "test_dup_intercept_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_duprateExpDensCurve_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "scatter2d": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test_duprateExpDens.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "session_info": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cd524e9e74304c2930cf28e2d741d351"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-11T11:21:56.741878886"
+    },
+    "sarscov2 - bam - paired_end": {
+        "content": [
+            "test_duprateExpBoxplot.pdf",
+            "test_expressionHist.pdf",
+            "test_duprateExpDens.pdf",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "strandedness": "forward"
+                    },
+                    "test_dupMatrix.txt:md5,5a327feaba56e5ea96a2cb7e8577e196"
+                ]
+            ],
+            null,
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "strandedness": "forward"
+                    },
+                    [
+                        "test_dup_intercept_mqc.txt:md5,002855b42a71aa0f407ef7fa19df9ac3",
+                        "test_duprateExpDensCurve_mqc.txt:md5,e797d8e256c5b2ab3aad1801360f1a77"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,cd524e9e74304c2930cf28e2d741d351"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-11T11:22:10.053957095"
+    },
+    "sarscov2 - bam - paired_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_duprateExpDens.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_duprateExpBoxplot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_expressionHist.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_dupMatrix.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_intercept_slope.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        [
+                            "test_dup_intercept_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_duprateExpDensCurve_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    "versions.yml:md5,cd524e9e74304c2930cf28e2d741d351"
+                ],
+                "boxplot": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_duprateExpBoxplot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "dupmatrix": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_dupMatrix.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "hist": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_expressionHist.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "intercept_slope": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_intercept_slope.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        [
+                            "test_dup_intercept_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_duprateExpDensCurve_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "scatter2d": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test_duprateExpDens.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "session_info": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "strandedness": "forward"
+                        },
+                        "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cd524e9e74304c2930cf28e2d741d351"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-11T11:22:22.134058061"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/dupradar/tests/nextflow.config b/modules/nf-core/dupradar/tests/nextflow.config
new file mode 100644
index 000000000..1b44170a0
--- /dev/null
+++ b/modules/nf-core/dupradar/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: DUPRADAR {
+        ext.args = { "--feature_type CDS" }
+    }
+    
+}
diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml
new file mode 100644
index 000000000..70389e664
--- /dev/null
+++ b/modules/nf-core/fastp/environment.yml
@@ -0,0 +1,7 @@
+name: fastp
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::fastp=0.23.4
diff --git a/modules/nf-core/fastp/fastp.diff b/modules/nf-core/fastp/fastp.diff
deleted file mode 100644
index b50d8e387..000000000
--- a/modules/nf-core/fastp/fastp.diff
+++ /dev/null
@@ -1,32 +0,0 @@
-Changes in module 'nf-core/fastp'
---- modules/nf-core/fastp/main.nf
-+++ modules/nf-core/fastp/main.nf
-@@ -45,7 +45,7 @@
-             $adapter_list \\
-             $fail_fastq \\
-             $args \\
--            2> ${prefix}.fastp.log \\
-+            2> >(tee ${prefix}.fastp.log >&2) \\
-         | gzip -c > ${prefix}.fastp.fastq.gz
- 
-         cat <<-END_VERSIONS > versions.yml
-@@ -66,7 +66,7 @@
-             $adapter_list \\
-             $fail_fastq \\
-             $args \\
--            2> ${prefix}.fastp.log
-+            2> >(tee ${prefix}.fastp.log >&2)
- 
-         cat <<-END_VERSIONS > versions.yml
-         "${task.process}":
-@@ -91,7 +91,7 @@
-             --thread $task.cpus \\
-             --detect_adapter_for_pe \\
-             $args \\
--            2> ${prefix}.fastp.log
-+            2> >(tee ${prefix}.fastp.log >&2)
- 
-         cat <<-END_VERSIONS > versions.yml
-         "${task.process}":
-
-************************************************************
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index 8cade07f0..e1b9f5656 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -2,7 +2,7 @@ process FASTP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::fastp=0.23.4"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' :
         'biocontainers/fastp:0.23.4--h5f740d0_0' }"
@@ -10,6 +10,7 @@ process FASTP {
     input:
     tuple val(meta), path(reads)
     path  adapter_fasta
+    val   discard_trimmed_pass
     val   save_trimmed_fail
     val   save_merged
 
@@ -18,9 +19,9 @@ process FASTP {
     tuple val(meta), path('*.json')           , emit: json
     tuple val(meta), path('*.html')           , emit: html
     tuple val(meta), path('*.log')            , emit: log
-    path "versions.yml"                       , emit: versions
     tuple val(meta), path('*.fail.fastq.gz')  , optional:true, emit: reads_fail
     tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged
+    path "versions.yml"                       , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,7 +30,9 @@ process FASTP {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def adapter_list = adapter_fasta ? "--adapter_fasta ${adapter_fasta}" : ""
-    def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
+    def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--failed_out ${prefix}.paired.fail.fastq.gz --unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
+    def out_fq1 = discard_trimmed_pass ?: ( meta.single_end ? "--out1 ${prefix}.fastp.fastq.gz" : "--out1 ${prefix}_1.fastp.fastq.gz" )
+    def out_fq2 = discard_trimmed_pass ?: "--out2 ${prefix}_2.fastp.fastq.gz"
     // Added soft-links to original fastqs for consistent naming in MultiQC
     // Use single ended for interleaved. Add --interleaved_in in config.
     if ( task.ext.args?.contains('--interleaved_in') ) {
@@ -59,7 +62,7 @@ process FASTP {
 
         fastp \\
             --in1 ${prefix}.fastq.gz \\
-            --out1  ${prefix}.fastp.fastq.gz \\
+            $out_fq1 \\
             --thread $task.cpus \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
@@ -81,8 +84,8 @@ process FASTP {
         fastp \\
             --in1 ${prefix}_1.fastq.gz \\
             --in2 ${prefix}_2.fastq.gz \\
-            --out1 ${prefix}_1.fastp.fastq.gz \\
-            --out2 ${prefix}_2.fastp.fastq.gz \\
+            $out_fq1 \\
+            $out_fq2 \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
             $adapter_list \\
@@ -99,4 +102,24 @@ process FASTP {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix              = task.ext.prefix ?: "${meta.id}"
+    def is_single_output    = task.ext.args?.contains('--interleaved_in') || meta.single_end
+    def touch_reads         = (discard_trimmed_pass) ? "" : (is_single_output) ? "echo '' | gzip > ${prefix}.fastp.fastq.gz" : "echo '' | gzip > ${prefix}_1.fastp.fastq.gz ; echo '' | gzip > ${prefix}_2.fastp.fastq.gz"
+    def touch_merged        = (!is_single_output && save_merged) ? "echo '' | gzip >  ${prefix}.merged.fastq.gz" : ""
+    def touch_fail_fastq    = (!save_trimmed_fail) ? "" : meta.single_end ? "echo '' | gzip > ${prefix}.fail.fastq.gz" : "echo '' | gzip > ${prefix}.paired.fail.fastq.gz ; echo '' | gzip > ${prefix}_1.fail.fastq.gz ; echo '' | gzip > ${prefix}_2.fail.fastq.gz"
+    """
+    $touch_reads
+    $touch_fail_fastq
+    $touch_merged
+    touch "${prefix}.fastp.json"
+    touch "${prefix}.fastp.html"
+    touch "${prefix}.fastp.log"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml
index 197ea7ca6..8dfecc184 100644
--- a/modules/nf-core/fastp/meta.yml
+++ b/modules/nf-core/fastp/meta.yml
@@ -27,13 +27,16 @@ input:
       type: file
       description: File in FASTA format containing possible adapters to remove.
       pattern: "*.{fasta,fna,fas,fa}"
+  - discard_trimmed_pass:
+      type: boolean
+      description: Specify true to not write any reads that pass trimming thresholds. |
+        This can be used to use fastp for the output report only.
   - save_trimmed_fail:
       type: boolean
       description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
   - save_merged:
       type: boolean
-      description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz`
-
+      description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz`
 output:
   - meta:
       type: map
@@ -71,3 +74,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test
new file mode 100644
index 000000000..c4e119aff
--- /dev/null
+++ b/modules/nf-core/fastp/tests/main.nf.test
@@ -0,0 +1,573 @@
+nextflow_process {
+
+    name "Test Process FASTP"
+    script "../main.nf"
+    process "FASTP"
+
+    test("test_fastp_single_end") {
+
+        when {
+
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") },
+                { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") },
+                { assert snapshot(
+                    process.out.json,
+                    process.out.reads,
+                    process.out.reads_fail,
+                    process.out.reads_merged,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end") {
+
+        when {
+
+            process {
+                """
+                adapter_fasta     = []
+                save_trimmed_pass = true
+                save_trimmed_fail = false
+                save_merged       = false
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") },
+                { assert path(process.out.log.get(0).get(1)).getText().contains("Q30 bases: 12281(88.3716%)") },
+                { assert snapshot(
+                    process.out.json,
+                    process.out.reads,
+                    process.out.reads_fail,
+                    process.out.reads_merged,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("fastp test_fastp_interleaved") {
+
+        config './nextflow.interleaved.config'
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.html.get(0).get(1)).getText().contains("paired end (151 cycles + 151 cycles)") },
+                { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 162") },
+                { assert process.out.reads_fail == [] },
+                { assert process.out.reads_merged == [] },
+                { assert snapshot(
+                    process.out.reads,
+                    process.out.json,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_fastp_single_end_trim_fail") {
+
+        when {
+
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = true
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") },
+                { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") },
+                { assert snapshot(
+                    process.out.json,
+                    process.out.reads,
+                    process.out.reads_fail,
+                    process.out.reads_merged,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end_trim_fail") {
+
+        config './nextflow.save_failed.config'
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = true
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") },
+                { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 162") },
+                { assert snapshot(
+                    process.out.reads,
+                    process.out.reads_fail,
+                    process.out.reads_merged,
+                    process.out.json,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end_merged") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = false
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") },
+                { assert path(process.out.log.get(0).get(1)).getText().contains("total reads: 75") },
+                { assert snapshot(
+                    process.out.json,
+                    process.out.reads,
+                    process.out.reads_fail,
+                    process.out.reads_merged,
+                    process.out.versions).match() },
+            )
+        }
+    }
+
+    test("test_fastp_paired_end_merged_adapterlist") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] =  Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ])
+                input[2] = false
+                input[3] = false
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.html.get(0).get(1)).getText().contains("<div id='After_filtering__merged__quality'>") },
+                { assert path(process.out.log.get(0).get(1)).getText().contains("total bases: 13683") },
+                { assert snapshot(
+                    process.out.json,
+                    process.out.reads,
+                    process.out.reads_fail,
+                    process.out.reads_merged,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_fastp_single_end_qc_only") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = true
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") },
+                { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") },
+                { assert snapshot(
+                    process.out.json,
+                    process.out.reads,
+                    process.out.reads,
+                    process.out.reads_fail,
+                    process.out.reads_fail,
+                    process.out.reads_merged,
+                    process.out.reads_merged,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end_qc_only") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = true
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") },
+                { assert path(process.out.log.get(0).get(1)).getText().contains("Q30 bases: 12281(88.3716%)") },
+                { assert snapshot(
+                    process.out.json,
+                    process.out.reads,
+                    process.out.reads,
+                    process.out.reads_fail,
+                    process.out.reads_fail,
+                    process.out.reads_merged,
+                    process.out.reads_merged,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_fastp_single_end - stub") {
+
+        options "-stub"
+
+        when {
+
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end - stub") {
+
+        options "-stub"
+
+        when {
+
+            process {
+                """
+                adapter_fasta     = []
+                save_trimmed_pass = true
+                save_trimmed_fail = false
+                save_merged       = false
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("fastp - stub test_fastp_interleaved") {
+
+        options "-stub"
+
+        config './nextflow.interleaved.config'
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fastp_single_end_trim_fail - stub") {
+
+        options "-stub"
+
+        when {
+
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = true
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end_trim_fail - stub") {
+
+        options "-stub"
+
+        config './nextflow.save_failed.config'
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = true
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end_merged - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = false
+                input[3] = false
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end_merged_adapterlist - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] =  Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ])
+                input[2] = false
+                input[3] = false
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fastp_single_end_qc_only - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = true
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fastp_paired_end_qc_only - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = []
+                input[2] = true
+                input[3] = false
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap
new file mode 100644
index 000000000..54be7e45f
--- /dev/null
+++ b/modules/nf-core/fastp/tests/main.nf.test.snap
@@ -0,0 +1,1331 @@
+{
+    "test_fastp_single_end_qc_only - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    
+                ],
+                "reads_fail": [
+                    
+                ],
+                "reads_merged": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T14:31:10.841098"
+    },
+    "test_fastp_paired_end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7",
+                        "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T13:43:28.665779"
+    },
+    "test_fastp_paired_end_merged_adapterlist": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,5914ca3f21ce162123a824e33e8564f6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672",
+                        "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5"
+                ]
+            ],
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T13:44:18.210375"
+    },
+    "test_fastp_single_end_qc_only": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.fastp.json:md5,5cc5f01e449309e0e689ed6f51a2294a"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T13:44:27.380974"
+    },
+    "test_fastp_paired_end_trim_fail": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,6ff32a64c5188b9a9192be1398c262c7",
+                        "test_2.fastp.fastq.gz:md5,db0cb7c9977e94ac2b4b446ebd017a8a"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.paired.fail.fastq.gz:md5,409b687c734cedd7a1fec14d316e1366",
+                        "test_1.fail.fastq.gz:md5,4f273cf3159c13f79e8ffae12f5661f6",
+                        "test_2.fail.fastq.gz:md5,f97b9edefb5649aab661fbc9e71fc995"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519"
+                ]
+            ],
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T13:43:58.749589"
+    },
+    "fastp - stub test_fastp_interleaved": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "reads_fail": [
+                    
+                ],
+                "reads_merged": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T13:50:00.270029"
+    },
+    "test_fastp_single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
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+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T13:43:38.910832"
+    },
+    "test_fastp_single_end_trim_fail": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.fastp.json:md5,9a7ee180f000e8d00c7fb67f06293eb5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.fail.fastq.gz:md5,3e4aaadb66a5b8fc9b881bf39c227abd"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T13:43:48.22378"
+    },
+    "test_fastp_paired_end_qc_only": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,623064a45912dac6f2b64e3f2e9901df"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T13:44:36.334938"
+    },
+    "test_fastp_paired_end_qc_only - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    
+                ],
+                "reads_fail": [
+                    
+                ],
+                "reads_merged": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T14:31:27.096468"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fastp/tests/nextflow.interleaved.config b/modules/nf-core/fastp/tests/nextflow.interleaved.config
new file mode 100644
index 000000000..4be8dbd2c
--- /dev/null
+++ b/modules/nf-core/fastp/tests/nextflow.interleaved.config
@@ -0,0 +1,5 @@
+process {
+    withName: FASTP {
+        ext.args = "--interleaved_in -e 30"
+    }
+}
diff --git a/modules/nf-core/fastp/tests/nextflow.save_failed.config b/modules/nf-core/fastp/tests/nextflow.save_failed.config
new file mode 100644
index 000000000..53b61b0c1
--- /dev/null
+++ b/modules/nf-core/fastp/tests/nextflow.save_failed.config
@@ -0,0 +1,5 @@
+process {
+    withName: FASTP {
+        ext.args = "-e 30"
+    }
+}
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
new file mode 100644
index 000000000..1787b38a9
--- /dev/null
+++ b/modules/nf-core/fastqc/environment.yml
@@ -0,0 +1,7 @@
+name: fastqc
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/fastqc.diff b/modules/nf-core/fastqc/fastqc.diff
deleted file mode 100644
index 0518d2b8f..000000000
--- a/modules/nf-core/fastqc/fastqc.diff
+++ /dev/null
@@ -1,23 +0,0 @@
-Changes in module 'nf-core/fastqc'
---- modules/nf-core/fastqc/main.nf
-+++ modules/nf-core/fastqc/main.nf
-@@ -37,7 +37,7 @@
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
--        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-+        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-     END_VERSIONS
-     """
- 
-@@ -49,7 +49,7 @@
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
--        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-+        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-     END_VERSIONS
-     """
- }
-
-************************************************************
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index c9f64702b..d8989f481 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -2,7 +2,7 @@ process FASTQC {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::fastqc=0.12.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' :
         'biocontainers/fastqc:0.12.1--hdfd78af_0' }"
@@ -25,6 +25,14 @@ process FASTQC {
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+
+    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
+    // FastQC memory value allowed range (100 - 10000)
+    def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
+
     """
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
@@ -33,6 +41,7 @@ process FASTQC {
     fastqc \\
         $args \\
         --threads $task.cpus \\
+        --memory $fastqc_memory \\
         $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 4da5bb5a0..ee5507e06 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -50,3 +50,8 @@ authors:
   - "@grst"
   - "@ewels"
   - "@FelixKrueger"
+maintainers:
+  - "@drpatelh"
+  - "@grst"
+  - "@ewels"
+  - "@FelixKrueger"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index badb67161..a67f92777 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -1,39 +1,304 @@
 nextflow_process {
 
     name "Test Process FASTQC"
-    script "modules/nf-core/fastqc/main.nf"
+    script "../main.nf"
     process "FASTQC"
-    tag "fastqc"
-    tag "modules_nfcore"
 
-    test("Single-Read") {
+    test("sarscov2 single-end [fastq]") {
 
         when {
-            params {
-                outdir   = "$outputDir"
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id: 'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
+                // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
+                // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
             }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+                { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+                { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2 single-end [fastq] - stub") {
+
+    options "-stub"
+        when {
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ id: 'test', single_end:true ],
-                    [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-                    ]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
                 """
             }
         }
 
         then {
             assertAll (
-            { assert process.success },
-            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
-            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
-            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-            { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" },
-            { assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert snapshot(process.out.versions).match("versions") },
-            { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 636a32cea..d5db3092f 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,10 +1,392 @@
 {
-    "versions": {
+    "sarscov2 custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
-        "timestamp": "2023-10-09T23:40:54+0000"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:16.374038"
+    },
+    "sarscov2 single-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:24.993809"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:03:10.93942"
+    },
+    "sarscov2 interleaved [fastq]": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:42.355718"
+    },
+    "sarscov2 paired-end [bam]": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:53.276274"
+    },
+    "sarscov2 multiple [fastq]": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:05.527626"
+    },
+    "sarscov2 paired-end [fastq]": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:31.188871"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:34.273566"
+    },
+    "sarscov2 multiple [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:03:02.304411"
+    },
+    "sarscov2 single-end [fastq]": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:19.095607"
+    },
+    "sarscov2 interleaved [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:44.640184"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:53.550742"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml
new file mode 100644
index 000000000..c588de38a
--- /dev/null
+++ b/modules/nf-core/fq/subsample/environment.yml
@@ -0,0 +1,7 @@
+name: fq_subsample
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::fq=0.9.1
diff --git a/modules/nf-core/fq/subsample/main.nf b/modules/nf-core/fq/subsample/main.nf
index 8b4ff5be0..a8e647bb1 100644
--- a/modules/nf-core/fq/subsample/main.nf
+++ b/modules/nf-core/fq/subsample/main.nf
@@ -2,7 +2,7 @@ process FQ_SUBSAMPLE {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::fq=0.9.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0':
         'biocontainers/fq:0.9.1--h9ee0642_0' }"
@@ -52,4 +52,16 @@ process FQ_SUBSAMPLE {
         fq: \$(echo \$(fq subsample --version | sed 's/fq-subsample //g'))
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo '' | gzip >  ${prefix}_R1.fastq.gz
+    echo '' | gzip >  ${prefix}_R2.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fq: \$(echo \$(fq subsample --version | sed 's/fq-subsample //g'))
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/fq/subsample/meta.yml b/modules/nf-core/fq/subsample/meta.yml
index 9d93f8df0..6c5e87f3e 100644
--- a/modules/nf-core/fq/subsample/meta.yml
+++ b/modules/nf-core/fq/subsample/meta.yml
@@ -2,16 +2,15 @@ name: "fq_subsample"
 description: fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args.
 keywords:
   - fastq
-  - sample
+  - fq
+  - subsample
 tools:
   - "fq":
       description: "fq is a library to generate and validate FASTQ file pairs."
       homepage: "https://github.com/stjude-rust-labs/fq"
       documentation: "https://github.com/stjude-rust-labs/fq"
       tool_dev_url: "https://github.com/stjude-rust-labs/fq"
-
-      licence: "['MIT']"
-
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -22,7 +21,6 @@ input:
       type: file
       description: FASTQ file
       pattern: "*.{fq,fastq}{,.gz}"
-
 output:
   - meta:
       type: map
@@ -37,6 +35,7 @@ output:
       type: file
       description: Randomly sampled FASTQ files.
       pattern: "*_R[12].fastq.gz"
-
 authors:
   - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
diff --git a/modules/nf-core/fq/subsample/tests/main.nf.test b/modules/nf-core/fq/subsample/tests/main.nf.test
new file mode 100644
index 000000000..13bb75945
--- /dev/null
+++ b/modules/nf-core/fq/subsample/tests/main.nf.test
@@ -0,0 +1,206 @@
+nextflow_process {
+
+    name "Test Process FQ_SUBSAMPLE"
+    script "../main.nf"
+    process "FQ_SUBSAMPLE"
+
+    test("test_fq_subsample_no_args") {
+        config "./nextflow_no_args.config"
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert !process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fq_subsample_probability") {
+        config "./nextflow_probability.config"
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fq_subsample_probability - stub") {
+        config "./nextflow_probability.config"
+        options "-stub"
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fq_subsample_record_count") {
+        config "./nextflow_record_count.config"
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fq_subsample_record_count - stub") {
+        config "./nextflow_record_count.config"
+        options "-stub"
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fq_subsample_single") {
+        config "./nextflow.config"
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fq_subsample_single - stub") {
+        config "./nextflow.config"
+        options "-stub"
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_fq_subsample_no_input") {
+        config "./nextflow.config"
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    []
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert !process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fq/subsample/tests/main.nf.test.snap b/modules/nf-core/fq/subsample/tests/main.nf.test.snap
new file mode 100644
index 000000000..739c626d7
--- /dev/null
+++ b/modules/nf-core/fq/subsample/tests/main.nf.test.snap
@@ -0,0 +1,411 @@
+{
+    "test_fq_subsample_probability - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T08:26:12.163153"
+    },
+    "test_fq_subsample_probability": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,19326ff922a16c0cb81191f2a0a5c5fc",
+                            "test_R2.fastq.gz:md5,ce7ff46296d89b68521ad55a3588bcfe"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,19326ff922a16c0cb81191f2a0a5c5fc",
+                            "test_R2.fastq.gz:md5,ce7ff46296d89b68521ad55a3588bcfe"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-17T17:57:15.446336"
+    },
+    "test_fq_subsample_single - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T08:26:55.736374"
+    },
+    "test_fq_subsample_no_args - sub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T08:25:42.190405"
+    },
+    "test_fq_subsample_record_count": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,394c7a233f1c1c1a167a34cf2895d26d",
+                            "test_R2.fastq.gz:md5,32724cbdb5ab954a0a659ebcd56ca422"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,394c7a233f1c1c1a167a34cf2895d26d",
+                            "test_R2.fastq.gz:md5,32724cbdb5ab954a0a659ebcd56ca422"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-17T17:57:23.920058"
+    },
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T17:16:10.090213"
+    },
+    "test_fq_subsample_single": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastq.gz:md5,19326ff922a16c0cb81191f2a0a5c5fc"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastq.gz:md5,19326ff922a16c0cb81191f2a0a5c5fc"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-17T17:57:31.908993"
+    },
+    "test_fq_subsample_no_args": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "fastq": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-10-17T11:17:09.761156"
+    },
+    "test_fq_subsample_no_input": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "fastq": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-10-17T11:17:37.555824"
+    },
+    "test_fq_subsample_record_count - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T08:26:33.873553"
+    },
+    "test_fq_subsample_no_input - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T08:27:21.793136"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fq/subsample/tests/nextflow.config b/modules/nf-core/fq/subsample/tests/nextflow.config
new file mode 100644
index 000000000..41edd9f1d
--- /dev/null
+++ b/modules/nf-core/fq/subsample/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: FQ_SUBSAMPLE {
+        ext.args = '--probability 0.1 -s 123'
+    }
+
+}
diff --git a/modules/nf-core/fq/subsample/tests/nextflow_no_args.config b/modules/nf-core/fq/subsample/tests/nextflow_no_args.config
new file mode 100644
index 000000000..88990d20c
--- /dev/null
+++ b/modules/nf-core/fq/subsample/tests/nextflow_no_args.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: FQ_SUBSAMPLE {
+        ext.args = ''
+    }
+
+}
diff --git a/modules/nf-core/fq/subsample/tests/nextflow_probability.config b/modules/nf-core/fq/subsample/tests/nextflow_probability.config
new file mode 100644
index 000000000..8cde0c77c
--- /dev/null
+++ b/modules/nf-core/fq/subsample/tests/nextflow_probability.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: FQ_SUBSAMPLE {
+        ext.args = '-p 0.1 -s 123'
+    }
+
+}
diff --git a/modules/nf-core/fq/subsample/tests/nextflow_record_count.config b/modules/nf-core/fq/subsample/tests/nextflow_record_count.config
new file mode 100644
index 000000000..1ea624e54
--- /dev/null
+++ b/modules/nf-core/fq/subsample/tests/nextflow_record_count.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: FQ_SUBSAMPLE {
+        ext.args = '-n 10 -s 123'
+    }
+
+}
diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml
new file mode 100644
index 000000000..c6df58ad0
--- /dev/null
+++ b/modules/nf-core/gffread/environment.yml
@@ -0,0 +1,7 @@
+name: gffread
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::gffread=0.12.7
diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf
index 68f8045b5..da55cbab7 100644
--- a/modules/nf-core/gffread/main.nf
+++ b/modules/nf-core/gffread/main.nf
@@ -1,30 +1,57 @@
 process GFFREAD {
-    tag "$gff"
+    tag "$meta.id"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' :
-        'biocontainers/gffread:0.12.1--h8b12597_0' }"
+        'https://depot.galaxyproject.org/singularity/gffread:0.12.7--hdcf5f25_4' :
+        'biocontainers/gffread:0.12.7--hdcf5f25_4' }"
 
     input:
-    path gff
+    tuple val(meta), path(gff)
+    path fasta
 
     output:
-    path "*.gtf"        , emit: gtf
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("*.gtf")  , emit: gtf             , optional: true
+    tuple val(meta), path("*.gff3") , emit: gffread_gff     , optional: true
+    tuple val(meta), path("*.fasta"), emit: gffread_fasta   , optional: true
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args   ?: ''
-    def prefix = task.ext.prefix ?: "${gff.baseName}"
+    def args        = task.ext.args             ?: ''
+    def prefix      = task.ext.prefix           ?: "${meta.id}"
+    def extension   = args.contains("-T")       ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' )
+    def fasta_arg   = fasta                     ? "-g $fasta" : ''
+    def output_name = "${prefix}.${extension}"
+    def output      = extension == "fasta"      ? "$output_name" : "-o $output_name"
+    def args_sorted = args.replaceAll(/(.*)(-[wxy])(.*)/) { all, pre, param, post -> "$pre $post $param" }.trim()
+    // args_sorted  = Move '-w', '-x', and '-y' to the end of the args string as gffread expects the file name after these parameters
+    if ( "$output_name" in [ "$gff", "$fasta" ] ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     gffread \\
         $gff \\
-        $args \\
-        -o ${prefix}.gtf
+        $fasta_arg \\
+        $args_sorted \\
+        $output
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gffread: \$(gffread --version 2>&1)
+    END_VERSIONS
+    """
+
+    stub:
+    def args        = task.ext.args             ?: ''
+    def prefix      = task.ext.prefix           ?: "${meta.id}"
+    def extension   = args.contains("-T")       ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' )
+    def output_name = "${prefix}.${extension}"
+    if ( "$output_name" in [ "$gff", "$fasta" ] ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    touch $output_name
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         gffread: \$(gffread --version 2>&1)
diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml
index f486f8bb5..c06028208 100644
--- a/modules/nf-core/gffread/meta.yml
+++ b/modules/nf-core/gffread/meta.yml
@@ -13,20 +13,43 @@ tools:
       doi: 10.12688/f1000research.23297.1
       licence: ["MIT"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing meta data
+        e.g. [ id:'test' ]
   - gff:
       type: file
       description: A reference file in either the GFF3, GFF2 or GTF format.
       pattern: "*.{gff, gtf}"
+  - fasta:
+      type: file
+      description: A multi-fasta file with the genomic sequences
+      pattern: "*.{fasta,fa,faa,fas,fsa}"
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing meta data
+        e.g. [ id:'test' ]
   - gtf:
       type: file
-      description: GTF file resulting from the conversion of the GFF input file
+      description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present
       pattern: "*.{gtf}"
+  - gffread_gff:
+      type: file
+      description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent
+      pattern: "*.gff3"
+  - gffread_fasta:
+      type: file
+      description: Fasta file produced when either of '-w', '-x', '-y' parameters is present
+      pattern: "*.fasta"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
-  - "@emiller88"
+  - "@edmundmiller"
 maintainers:
-  - "@emiller88"
+  - "@edmundmiller"
+  - "@gallvp"
diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test
new file mode 100644
index 000000000..e03820f4d
--- /dev/null
+++ b/modules/nf-core/gffread/tests/main.nf.test
@@ -0,0 +1,219 @@
+nextflow_process {
+
+    name "Test Process GFFREAD"
+    script "../main.nf"
+    process "GFFREAD"
+
+    test("sarscov2-gff3-gtf") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.gffread_gff == [] },
+                { assert process.out.gffread_fasta == [] }
+            )
+        }
+
+    }
+
+    test("sarscov2-gff3-gtf-stub") {
+
+        options '-stub'
+        config "./nextflow.config"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.gffread_gff == [] },
+                { assert process.out.gffread_fasta == [] }
+            )
+        }
+
+    }
+
+    test("sarscov2-gff3-gff3") {
+
+        config "./nextflow-gff3.config"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.gtf == [] },
+                { assert process.out.gffread_fasta == [] }
+            )
+        }
+
+    }
+
+    test("sarscov2-gff3-gff3-stub") {
+
+        options '-stub'
+        config "./nextflow-gff3.config"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.gtf == [] },
+                { assert process.out.gffread_fasta == [] }
+            )
+        }
+
+    }
+
+    test("sarscov2-gff3-fasta") {
+
+        config "./nextflow-fasta.config"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.gtf == [] },
+                { assert process.out.gffread_gff == [] }
+            )
+        }
+
+    }
+
+    test("sarscov2-gff3-fasta-stub") {
+
+        options '-stub'
+        config "./nextflow-fasta.config"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.gtf == [] },
+                { assert process.out.gffread_gff == [] }
+            )
+        }
+
+    }
+
+    test("sarscov2-gff3-fasta-fail-catch") {
+
+        options '-stub'
+        config "./nextflow-fasta.config"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: 'genome'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert ! process.success },
+                { assert process.stdout.toString().contains("Input and output names are the same") }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gffread/tests/main.nf.test.snap b/modules/nf-core/gffread/tests/main.nf.test.snap
new file mode 100644
index 000000000..15262320d
--- /dev/null
+++ b/modules/nf-core/gffread/tests/main.nf.test.snap
@@ -0,0 +1,272 @@
+{
+    "sarscov2-gff3-gtf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gtf:md5,1ea0ae98d3388e0576407dc4a24ef428"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ],
+                "gffread_fasta": [
+                    
+                ],
+                "gffread_gff": [
+                    
+                ],
+                "gtf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gtf:md5,1ea0ae98d3388e0576407dc4a24ef428"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-09T10:48:56.496187"
+    },
+    "sarscov2-gff3-gff3": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,c4e5da6267c6bee5899a2c204ae1ad91"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ],
+                "gffread_fasta": [
+                    
+                ],
+                "gffread_gff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,c4e5da6267c6bee5899a2c204ae1ad91"
+                    ]
+                ],
+                "gtf": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-09T10:49:00.892782"
+    },
+    "sarscov2-gff3-gtf-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ],
+                "gffread_fasta": [
+                    
+                ],
+                "gffread_gff": [
+                    
+                ],
+                "gtf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-09T11:11:26.975666"
+    },
+    "sarscov2-gff3-fasta-stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ],
+                "gffread_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gffread_gff": [
+                    
+                ],
+                "gtf": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-09T11:11:44.34792"
+    },
+    "sarscov2-gff3-gff3-stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ],
+                "gffread_fasta": [
+                    
+                ],
+                "gffread_gff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gtf": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-09T11:11:35.221671"
+    },
+    "sarscov2-gff3-fasta": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,5f8108fb51739a0588ccf0a251de919a"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ],
+                "gffread_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,5f8108fb51739a0588ccf0a251de919a"
+                    ]
+                ],
+                "gffread_gff": [
+                    
+                ],
+                "gtf": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-09T10:54:02.88143"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gffread/tests/nextflow-fasta.config b/modules/nf-core/gffread/tests/nextflow-fasta.config
new file mode 100644
index 000000000..ac6cb1484
--- /dev/null
+++ b/modules/nf-core/gffread/tests/nextflow-fasta.config
@@ -0,0 +1,5 @@
+process {
+    withName: GFFREAD {
+        ext.args = '-w -S'
+    }
+}
diff --git a/modules/nf-core/gffread/tests/nextflow-gff3.config b/modules/nf-core/gffread/tests/nextflow-gff3.config
new file mode 100644
index 000000000..afe0830e5
--- /dev/null
+++ b/modules/nf-core/gffread/tests/nextflow-gff3.config
@@ -0,0 +1,5 @@
+process {
+    withName: GFFREAD {
+        ext.args = ''
+    }
+}
diff --git a/modules/nf-core/gffread/tests/nextflow.config b/modules/nf-core/gffread/tests/nextflow.config
new file mode 100644
index 000000000..74b25094f
--- /dev/null
+++ b/modules/nf-core/gffread/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: GFFREAD {
+        ext.args = '-T'
+    }
+}
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
new file mode 100644
index 000000000..dfc02a7b5
--- /dev/null
+++ b/modules/nf-core/gunzip/environment.yml
@@ -0,0 +1,9 @@
+name: gunzip
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::grep=3.11
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
index 73bf08cde..5e67e3b9b 100644
--- a/modules/nf-core/gunzip/main.nf
+++ b/modules/nf-core/gunzip/main.nf
@@ -2,10 +2,10 @@ process GUNZIP {
     tag "$archive"
     label 'process_single'
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:22.04' :
+        'nf-core/ubuntu:22.04' }"
 
     input:
     tuple val(meta), path(archive)
@@ -18,8 +18,11 @@ process GUNZIP {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    gunzip = archive.toString() - '.gz'
+    def args        = task.ext.args ?: ''
+    def extension   = ( archive.toString() - '.gz' ).tokenize('.')[-1]
+    def name        = archive.toString() - '.gz' - ".$extension"
+    def prefix      = task.ext.prefix ?: name
+    gunzip          = prefix + ".$extension"
     """
     # Not calling gunzip itself because it creates files
     # with the original group ownership rather than the
@@ -37,7 +40,11 @@ process GUNZIP {
     """
 
     stub:
-    gunzip = archive.toString() - '.gz'
+    def args        = task.ext.args ?: ''
+    def extension   = ( archive.toString() - '.gz' ).tokenize('.')[-1]
+    def name        = archive.toString() - '.gz' - ".$extension"
+    def prefix      = task.ext.prefix ?: name
+    gunzip          = prefix + ".$extension"
     """
     touch $gunzip
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
index 4cdcdf4c4..f32973a0a 100644
--- a/modules/nf-core/gunzip/meta.yml
+++ b/modules/nf-core/gunzip/meta.yml
@@ -33,3 +33,8 @@ authors:
   - "@joseespinosa"
   - "@drpatelh"
   - "@jfy133"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
+  - "@gallvp"
diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test
new file mode 100644
index 000000000..384edf226
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/main.nf.test
@@ -0,0 +1,118 @@
+nextflow_process {
+
+    name "Test Process GUNZIP"
+    script "../main.nf"
+    process "GUNZIP"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("Should run without failures - prefix") {
+
+        config './nextflow.config'
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [ id: 'test' ],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("Should run without failures - stub") {
+
+        options '-stub'
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("Should run without failures - prefix - stub") {
+
+        options '-stub'
+        config './nextflow.config'
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [ id: 'test' ],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap
new file mode 100644
index 000000000..069967e76
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/main.nf.test.snap
@@ -0,0 +1,134 @@
+{
+    "Should run without failures - prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-25T11:35:10.861293"
+    },
+    "Should run without failures - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-25T11:35:05.857145"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-10-17T15:35:37.690477896"
+    },
+    "Should run without failures - prefix": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-25T11:33:32.921739"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config
new file mode 100644
index 000000000..dec776425
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: GUNZIP {
+        ext.prefix = { "${meta.id}.xyz" }
+    }
+}
diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml
new file mode 100644
index 000000000..0c1415f94
--- /dev/null
+++ b/modules/nf-core/hisat2/align/environment.yml
@@ -0,0 +1,8 @@
+name: hisat2_align
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hisat2=2.2.1
+  - bioconda::samtools=1.16.1
diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf
index db8e8bb6d..ea186f62a 100644
--- a/modules/nf-core/hisat2/align/main.nf
+++ b/modules/nf-core/hisat2/align/main.nf
@@ -3,7 +3,7 @@ process HISAT2_ALIGN {
     label 'process_high'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' :
         'biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' }"
@@ -90,4 +90,23 @@ process HISAT2_ALIGN {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def unaligned = params.save_unaligned ? "echo '' | gzip >  ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip >  ${prefix}.unmapped_2.fastq.gz" : ''
+    def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    ${unaligned}
+
+    touch ${prefix}.hisat2.summary.log
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hisat2: $VERSION
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+
 }
diff --git a/modules/nf-core/hisat2/align/meta.yml b/modules/nf-core/hisat2/align/meta.yml
index 008a9611f..b23eab75b 100644
--- a/modules/nf-core/hisat2/align/meta.yml
+++ b/modules/nf-core/hisat2/align/meta.yml
@@ -5,7 +5,6 @@ keywords:
   - fasta
   - genome
   - reference
-
 tools:
   - hisat2:
       description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
@@ -13,7 +12,6 @@ tools:
       documentation: https://daehwankimlab.github.io/hisat2/manual/
       doi: "10.1038/s41587-019-0201-4"
       licence: ["MIT"]
-
 input:
   - meta:
       type: map
@@ -43,7 +41,6 @@ input:
       type: file
       description: Splices sites in gtf file
       pattern: "*.{txt}"
-
 output:
   - meta:
       type: map
@@ -62,7 +59,9 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@ntoda03"
   - "@ramprasadn"
+maintainers:
+  - "@ntoda03"
+  - "@ramprasadn"
diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test b/modules/nf-core/hisat2/align/tests/main.nf.test
new file mode 100644
index 000000000..8193c82d8
--- /dev/null
+++ b/modules/nf-core/hisat2/align/tests/main.nf.test
@@ -0,0 +1,414 @@
+nextflow_process {
+
+    name "Test Process HISAT2_ALIGN"
+    script "../main.nf"
+    process "HISAT2_ALIGN"
+
+    test("Single-End") {
+
+        setup {
+            run("HISAT2_EXTRACTSPLICESITES") {
+                script "../../extractsplicesites/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                """
+                }
+            }
+
+            run("HISAT2_BUILD") {
+                script "../../build/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = Channel.of([ [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.summary).match("se_summary") },
+                { assert snapshot(process.out.fastq).match("se_fastq") },
+                { assert snapshot(process.out.versions).match("se_versions") }
+            )
+        }
+    }
+
+    test("Single-End - stub") {
+        options "-stub"
+
+        setup {
+            run("HISAT2_EXTRACTSPLICESITES") {
+                script "../../extractsplicesites/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                """
+                }
+            }
+
+            run("HISAT2_BUILD") {
+                script "../../build/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = Channel.of([ [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Paired-End") {
+
+        setup {
+            run("HISAT2_EXTRACTSPLICESITES") {
+                script "../../extractsplicesites/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                """
+                }
+            }
+
+            run("HISAT2_BUILD") {
+                script "../../build/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = Channel.of([ [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.summary).match("pe_summary") },
+                { assert snapshot(process.out.fastq).match("pe_fastq") },
+                { assert snapshot(process.out.versions).match("pe_versions") }
+            )
+        }
+    }
+
+    test("Paired-End - stub") {
+        options "-stub"
+
+        setup {
+            run("HISAT2_EXTRACTSPLICESITES") {
+                script "../../extractsplicesites/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                """
+                }
+            }
+
+            run("HISAT2_BUILD") {
+                script "../../build/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = Channel.of([ [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Single-End No Splice Sites") {
+
+        setup {
+            run("HISAT2_BUILD") {
+                script "../../build/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = [[:],[]]
+                input[2] = [[:],[]]
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.summary).match("se_no_ss_summary") },
+                { assert snapshot(process.out.fastq).match("se_no_ss_fastq") },
+                { assert snapshot(process.out.versions).match("se_no_ss_versions") }
+            )
+        }
+    }
+
+    test("Single-End No Splice Sites - stub") {
+        options "-stub"
+
+        setup {
+            run("HISAT2_BUILD") {
+                script "../../build/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = [[:],[]]
+                input[2] = [[:],[]]
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Paired-End No Splice Sites") {
+
+        setup {
+            run("HISAT2_BUILD") {
+                script "../../build/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = [[:],[]]
+                input[2] = [[:],[]]
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.summary).match("pe_no_ss_summary") },
+                { assert snapshot(process.out.fastq).match("pe_no_ss_fastq") },
+                { assert snapshot(process.out.versions).match("pe_no_ss_versions") }
+            )
+        }
+    }
+
+    test("Paired-End No Splice Sites - stub") {
+        options "-stub"
+
+        setup {
+            run("HISAT2_BUILD") {
+                script "../../build/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = [[:],[]]
+                input[2] = [[:],[]]
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test.snap b/modules/nf-core/hisat2/align/tests/main.nf.test.snap
new file mode 100644
index 000000000..ff670d452
--- /dev/null
+++ b/modules/nf-core/hisat2/align/tests/main.nf.test.snap
@@ -0,0 +1,406 @@
+{
+    "se_versions": {
+        "content": [
+            [
+                "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:08:33.735489"
+    },
+    "Paired-End - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastq": [
+                    
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:14.35626"
+    },
+    "Single-End - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastq": [
+                    
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:08:47.404885"
+    },
+    "pe_no_ss_versions": {
+        "content": [
+            [
+                "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:52.076955"
+    },
+    "Paired-End No Splice Sites - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastq": [
+                    
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:10:03.739697"
+    },
+    "pe_no_ss_summary": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.hisat2.summary.log:md5,9839b31db795958cc4b70711a3414e9c"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:52.068244"
+    },
+    "pe_no_ss_fastq": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:52.072985"
+    },
+    "se_summary": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.hisat2.summary.log:md5,7b8a9e61b7646da1089b041333c41a87"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:08:33.727355"
+    },
+    "pe_summary": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.hisat2.summary.log:md5,9839b31db795958cc4b70711a3414e9c"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:01.495439"
+    },
+    "pe_fastq": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:01.500755"
+    },
+    "se_fastq": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:08:33.732523"
+    },
+    "se_no_ss_summary": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.hisat2.summary.log:md5,7b8a9e61b7646da1089b041333c41a87"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:26.851884"
+    },
+    "se_no_ss_versions": {
+        "content": [
+            [
+                "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:26.89234"
+    },
+    "se_no_ss_fastq": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:26.871369"
+    },
+    "Single-End No Splice Sites - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastq": [
+                    
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:39.544807"
+    },
+    "pe_versions": {
+        "content": [
+            [
+                "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:09:01.506346"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml
new file mode 100644
index 000000000..2e67cd3ea
--- /dev/null
+++ b/modules/nf-core/hisat2/build/environment.yml
@@ -0,0 +1,7 @@
+name: hisat2_build
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hisat2=2.2.1
diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf
index 90f8efcc6..17d8fdd5b 100644
--- a/modules/nf-core/hisat2/build/main.nf
+++ b/modules/nf-core/hisat2/build/main.nf
@@ -4,7 +4,7 @@ process HISAT2_BUILD {
     label 'process_high_memory'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::hisat2=2.2.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' :
         'biocontainers/hisat2:2.2.1--h1b792b2_3' }"
@@ -61,4 +61,15 @@ process HISAT2_BUILD {
         hisat2: $VERSION
     END_VERSIONS
     """
+
+    stub:
+    def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    mkdir hisat2
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hisat2: $VERSION
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml
index e61bf2a3f..6c28eb21c 100644
--- a/modules/nf-core/hisat2/build/meta.yml
+++ b/modules/nf-core/hisat2/build/meta.yml
@@ -13,7 +13,6 @@ tools:
       documentation: https://daehwankimlab.github.io/hisat2/manual/
       doi: "10.1038/s41587-019-0201-4"
       licence: ["MIT"]
-
 input:
   - meta:
       type: map
@@ -42,7 +41,6 @@ input:
       type: file
       description: Splices sites in gtf file
       pattern: "*.{txt}"
-
 output:
   - meta:
       type: map
@@ -57,6 +55,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@ntoda03"
+maintainers:
+  - "@ntoda03"
diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test b/modules/nf-core/hisat2/build/tests/main.nf.test
new file mode 100644
index 000000000..bd8e9dae0
--- /dev/null
+++ b/modules/nf-core/hisat2/build/tests/main.nf.test
@@ -0,0 +1,93 @@
+nextflow_process {
+
+    name "Test Process HISAT2_BUILD"
+    script "../main.nf"
+    process "HISAT2_BUILD"
+
+    test("Should run without failures") {
+
+        setup {
+            run("HISAT2_EXTRACTSPLICESITES") {
+                script "../../extractsplicesites/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = Channel.of([ [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Should run without failures - stub") {
+
+        options "-stub"
+
+        setup {
+            run("HISAT2_EXTRACTSPLICESITES") {
+                script "../../extractsplicesites/main.nf"
+                process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = Channel.of([ [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test.snap b/modules/nf-core/hisat2/build/tests/main.nf.test.snap
new file mode 100644
index 000000000..0e3b5c57f
--- /dev/null
+++ b/modules/nf-core/hisat2/build/tests/main.nf.test.snap
@@ -0,0 +1,113 @@
+{
+    "test - stub": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "index": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T17:29:31.567024"
+    },
+    "Should run without failures - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        [
+
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        [
+
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T18:18:08.896422"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        [
+                            "genome.1.ht2:md5,057cfa8a22b97ee9cff4c8d342498803",
+                            "genome.2.ht2:md5,47b153cd1319abc88dda532462651fcf",
+                            "genome.3.ht2:md5,4ed93abba181d8dfab2e303e33114777",
+                            "genome.4.ht2:md5,c25be5f8b0378abf7a58c8a880b87626",
+                            "genome.5.ht2:md5,91198831aaba993acac1734138c5f173",
+                            "genome.6.ht2:md5,265e1284ce85686516fae5d35540994a",
+                            "genome.7.ht2:md5,9013eccd91ad614d7893c739275a394f",
+                            "genome.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        [
+                            "genome.1.ht2:md5,057cfa8a22b97ee9cff4c8d342498803",
+                            "genome.2.ht2:md5,47b153cd1319abc88dda532462651fcf",
+                            "genome.3.ht2:md5,4ed93abba181d8dfab2e303e33114777",
+                            "genome.4.ht2:md5,c25be5f8b0378abf7a58c8a880b87626",
+                            "genome.5.ht2:md5,91198831aaba993acac1734138c5f173",
+                            "genome.6.ht2:md5,265e1284ce85686516fae5d35540994a",
+                            "genome.7.ht2:md5,9013eccd91ad614d7893c739275a394f",
+                            "genome.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-10-16T14:42:22.381609786"
+    }
+}
diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml
new file mode 100644
index 000000000..4b03e5e46
--- /dev/null
+++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml
@@ -0,0 +1,7 @@
+name: hisat2_extractsplicesites
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hisat2=2.2.1
diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf
index a6e59e202..588a9947a 100644
--- a/modules/nf-core/hisat2/extractsplicesites/main.nf
+++ b/modules/nf-core/hisat2/extractsplicesites/main.nf
@@ -3,7 +3,7 @@ process HISAT2_EXTRACTSPLICESITES {
     label 'process_medium'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::hisat2=2.2.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' :
         'biocontainers/hisat2:2.2.1--h1b792b2_3' }"
@@ -28,4 +28,15 @@ process HISAT2_EXTRACTSPLICESITES {
         hisat2: $VERSION
     END_VERSIONS
     """
+
+    stub:
+    def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${gtf.baseName}.splice_sites.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hisat2: $VERSION
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/hisat2/extractsplicesites/meta.yml b/modules/nf-core/hisat2/extractsplicesites/meta.yml
index f70de082a..40d77ce00 100644
--- a/modules/nf-core/hisat2/extractsplicesites/meta.yml
+++ b/modules/nf-core/hisat2/extractsplicesites/meta.yml
@@ -5,7 +5,6 @@ keywords:
   - gtf
   - genome
   - reference
-
 tools:
   - hisat2:
       description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
@@ -13,7 +12,6 @@ tools:
       documentation: https://daehwankimlab.github.io/hisat2/manual/
       doi: "10.1038/s41587-019-0201-4"
       licence: ["MIT"]
-
 input:
   - meta:
       type: map
@@ -24,7 +22,6 @@ input:
       type: file
       description: Reference gtf annotation file
       pattern: "*.{gtf}"
-
 output:
   - meta:
       type: map
@@ -39,7 +36,9 @@ output:
       type: file
       description: Splices sites in gtf file
       pattern: "*.{splice_sites.txt}"
-
 authors:
   - "@ntoda03"
   - "@ramprasadn"
+maintainers:
+  - "@ntoda03"
+  - "@ramprasadn"
diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test
new file mode 100644
index 000000000..a9f93ec52
--- /dev/null
+++ b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test
@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process HISAT2_EXTRACTSPLICESITES"
+    script "../main.nf"
+    process "HISAT2_EXTRACTSPLICESITES"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path("${process.out.txt[0][1]}").exists() },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [id:'genome'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap
new file mode 100644
index 000000000..1dcd8af23
--- /dev/null
+++ b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap
@@ -0,0 +1,47 @@
+{
+    "test - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        "genome.splice_sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,eeea7231fe197810659b8bad4133aff2"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        "genome.splice_sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,eeea7231fe197810659b8bad4133aff2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T17:34:13.229903"
+    },
+    "Should run without failures": {
+        "content": [
+            [
+                "versions.yml:md5,eeea7231fe197810659b8bad4133aff2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-18T20:56:30.71763"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf
index 28a47dbeb..bbd226c93 100644
--- a/modules/nf-core/kallisto/index/main.nf
+++ b/modules/nf-core/kallisto/index/main.nf
@@ -34,7 +34,7 @@ process KALLISTO_INDEX {
 
     stub:
     """
-    touch kallisto
+    mkdir kallisto
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test b/modules/nf-core/kallisto/index/tests/main.nf.test
index 97933d697..c5e86e87c 100644
--- a/modules/nf-core/kallisto/index/tests/main.nf.test
+++ b/modules/nf-core/kallisto/index/tests/main.nf.test
@@ -3,20 +3,16 @@ nextflow_process {
     name "Test Process KALLISTO_INDEX"
     script "../main.nf"
     process "KALLISTO_INDEX"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "kallisto"
-    tag "kallisto/index"
 
-    test("homo_sapiens genome_fasta") {
+    test("sarscov2 transcriptome.fasta") {
 
         when {
             process {
                 """
-                input[0] = [
-                    [ id:'test_fasta' ], // meta map
-                    [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
-                ]
+                input[0] = Channel.of([
+                    [ id:'transcriptome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
+                ])
                 """
             }
         }
@@ -27,7 +23,28 @@ nextflow_process {
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
 
+    test("sarscov2 transcriptome.fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'transcriptome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test.snap b/modules/nf-core/kallisto/index/tests/main.nf.test.snap
index c0f45ac45..b2891a4a3 100644
--- a/modules/nf-core/kallisto/index/tests/main.nf.test.snap
+++ b/modules/nf-core/kallisto/index/tests/main.nf.test.snap
@@ -1,13 +1,15 @@
 {
-    "homo_sapiens genome_fasta": {
+    "sarscov2 transcriptome.fasta - stub": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test_fasta"
+                            "id": "transcriptome"
                         },
-                        "kallisto:md5,2dab84e1456201beca5a43f4c514d67c"
+                        [
+                            
+                        ]
                     ]
                 ],
                 "1": [
@@ -16,9 +18,11 @@
                 "index": [
                     [
                         {
-                            "id": "test_fasta"
+                            "id": "transcriptome"
                         },
-                        "kallisto:md5,2dab84e1456201beca5a43f4c514d67c"
+                        [
+                            
+                        ]
                     ]
                 ],
                 "versions": [
@@ -26,6 +30,43 @@
                 ]
             }
         ],
-        "timestamp": "2023-11-02T09:58:48.83625986"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:27:54.464205"
+    },
+    "sarscov2 transcriptome.fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "transcriptome"
+                        },
+                        "kallisto:md5,ba657b396f8449f5c85b0563cdaa8346"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,178f9b57d4228edc356911d571b958a4"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "transcriptome"
+                        },
+                        "kallisto:md5,ba657b396f8449f5c85b0563cdaa8346"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,178f9b57d4228edc356911d571b958a4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-01-19T09:17:56.733532"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/kallisto/index/tests/tags.yml b/modules/nf-core/kallisto/index/tests/tags.yml
deleted file mode 100644
index 9f47b88a1..000000000
--- a/modules/nf-core/kallisto/index/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-kallisto/index:
-  - modules/nf-core/kallisto/index/**
diff --git a/modules/nf-core/kallisto/quant/main.nf b/modules/nf-core/kallisto/quant/main.nf
index f5444d791..acfc8c9c7 100644
--- a/modules/nf-core/kallisto/quant/main.nf
+++ b/modules/nf-core/kallisto/quant/main.nf
@@ -69,7 +69,13 @@ process KALLISTO_QUANT {
     """
 
     stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+
     """
+    mkdir -p $prefix
+    touch ${prefix}.log
+    touch ${prefix}.run_info.json
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         kallisto: \$(echo \$(kallisto version) | sed "s/kallisto, version //g" )
diff --git a/modules/nf-core/kallisto/quant/tests/main.nf.test b/modules/nf-core/kallisto/quant/tests/main.nf.test
index f716e5e6d..ec6e3d60c 100644
--- a/modules/nf-core/kallisto/quant/tests/main.nf.test
+++ b/modules/nf-core/kallisto/quant/tests/main.nf.test
@@ -3,44 +3,51 @@ nextflow_process {
     name "Test Process KALLISTO_QUANT"
     script "../main.nf"
     process "KALLISTO_QUANT"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "kallisto"
-    tag "kallisto/quant"
 
     setup {
             run("KALLISTO_INDEX") {
                 script "../../index/main.nf"
                 process {
-                """
-                input[0] = [
-                    [ id:'test_fasta' ], // meta map
-                    [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-                ]
-                """
+                    """
+                    input[0] = Channel.of([
+                        [ id:'transcriptome' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
+                    ])
+                    """
+                }
             }
+
+            run("KALLISTO_INDEX", alias: "KALLISTO_INDEX_STUB") {
+                script "../../index/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'transcriptome' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
+                    ])
+                    """
+                }
             }
         }
 
     test("sarscov2 single-end") {
-        config "./single_end.config"
-
         when {
-            params{
-                outdir = "$outputDir"
-            }
-
             process {
                 """
-                input[0] = [
+                gtf                = []
+                chromosomes        = []
+                fragment_length    = 150
+                fragment_length_sd = 75
+
+                input[0] = Channel.of([
                     [ id:'test', single_end:true ],
-                    [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
                 input[1] = KALLISTO_INDEX.out.index
-                input[2] = []
-                input[3] = []
-                input[4] = 150
-                input[5] = 75
+                input[2] = gtf
+                input[3] = chromosomes
+                input[4] = fragment_length
+                input[5] = fragment_length_sd
                 """
             }
         }
@@ -48,44 +55,109 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(path("$outputDir/kallisto/test/abundance.tsv")).match("abundance_tsv_single") },
-                { assert snapshot(process.out.log).match("se_log") },
-                { assert snapshot(process.out.versions).match("se_versions") }
+                { assert snapshot(
+                    path("${process.out.results[0][1]}/abundance.tsv"),
+                    process.out.log,
+                    process.out.versions).match() }
             )
         }
     }
 
     test("sarscov2 paired-end") {
-        config "./paired_end.config"
+        when {
+            process {
+                """
+                gtf                = []
+                chromosomes        = []
+                fragment_length    = []
+                fragment_length_sd = []
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = KALLISTO_INDEX.out.index
+                input[2] = gtf
+                input[3] = chromosomes
+                input[4] = fragment_length
+                input[5] = fragment_length_sd
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path("${process.out.results[0][1]}/abundance.tsv"),
+                    process.out.log,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2 single-end - stub") {
+
+        options "-stub"
 
         when {
-            params{
-                outdir = "$outputDir"
+            process {
+                """
+                gtf                = []
+                chromosomes        = []
+                fragment_length    = 150
+                fragment_length_sd = 75
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = KALLISTO_INDEX_STUB.out.index
+                input[2] = gtf
+                input[3] = chromosomes
+                input[4] = fragment_length
+                input[5] = fragment_length_sd
+                """
             }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 
+    test("sarscov2 paired-end - stub") {
+
+        options "-stub"
+
+        when {
             process {
                 """
-                input[0] = [
+                gtf                = []
+                chromosomes        = []
+                fragment_length    = []
+                fragment_length_sd = []
+
+                input[0] = Channel.of([
                     [ id:'test', single_end:false ], // meta map
-                    [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-                    ]
-                ]
-                input[1] = KALLISTO_INDEX.out.index
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = KALLISTO_INDEX_STUB.out.index
+                input[2] = gtf
+                input[3] = chromosomes
+                input[4] = fragment_length
+                input[5] = fragment_length_sd
                 """
             }
         }
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(path("$outputDir/kallisto/test/abundance.tsv")).match("abundance_tsv_paired") },
-                { assert snapshot(process.out.log).match("pe_log") },
-                { assert snapshot(process.out.versions).match("pe_versions") }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/nf-core/kallisto/quant/tests/main.nf.test.snap b/modules/nf-core/kallisto/quant/tests/main.nf.test.snap
index d59d7f06f..cf0d73304 100644
--- a/modules/nf-core/kallisto/quant/tests/main.nf.test.snap
+++ b/modules/nf-core/kallisto/quant/tests/main.nf.test.snap
@@ -1,6 +1,7 @@
 {
-    "pe_log": {
+    "sarscov2 paired-end": {
         "content": [
+            "abundance.tsv:md5,f0a9a2543f8fc0c8442be0a939d70f66",
             [
                 [
                     {
@@ -9,26 +10,170 @@
                     },
                     "test.log:md5,8a5987f8e779cd12ca708e2212f771f5"
                 ]
+            ],
+            [
+                "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94"
             ]
         ],
-        "timestamp": "2023-11-02T09:16:05.163403975"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:25:27.043048"
     },
-    "se_versions": {
+    "sarscov2 paired-end - stub": {
         "content": [
-            [
-                "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.run_info.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94"
+                ],
+                "json_info": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.run_info.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94"
+                ]
+            }
         ],
-        "timestamp": "2023-10-30T22:11:17.982220232"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:26:04.484652"
     },
-    "abundance_tsv_paired": {
+    "sarscov2 single-end - stub": {
         "content": [
-            "abundance.tsv:md5,f0a9a2543f8fc0c8442be0a939d70f66"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.run_info.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94"
+                ],
+                "json_info": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.run_info.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94"
+                ]
+            }
         ],
-        "timestamp": "2023-11-02T09:16:05.157883165"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:25:46.479136"
     },
-    "se_log": {
+    "sarscov2 single-end": {
         "content": [
+            "abundance.tsv:md5,8a4afe91e6a75b4e619daaf664eb7d9b",
             [
                 [
                     {
@@ -37,22 +182,15 @@
                     },
                     "test.log:md5,9c166f0c50cd4fdbdbf1bff9d5d8aba2"
                 ]
-            ]
-        ],
-        "timestamp": "2023-10-30T22:11:17.973230763"
-    },
-    "abundance_tsv_single": {
-        "content": [
-            "abundance.tsv:md5,8a4afe91e6a75b4e619daaf664eb7d9b"
-        ],
-        "timestamp": "2023-11-02T09:01:51.48615229"
-    },
-    "pe_versions": {
-        "content": [
+            ],
             [
                 "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94"
             ]
         ],
-        "timestamp": "2023-11-02T09:16:05.168753684"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:25:08.348876"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/kallisto/quant/tests/tags.yml b/modules/nf-core/kallisto/quant/tests/tags.yml
deleted file mode 100644
index 460936583..000000000
--- a/modules/nf-core/kallisto/quant/tests/tags.yml
+++ /dev/null
@@ -1,3 +0,0 @@
-kallisto/quant:
-  - modules/nf-core/kallisto/index/**
-  - modules/nf-core/kallisto/quant/**
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
new file mode 100644
index 000000000..a31464c97
--- /dev/null
+++ b/modules/nf-core/multiqc/environment.yml
@@ -0,0 +1,7 @@
+name: multiqc
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::multiqc=1.24.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
new file mode 100644
index 000000000..ceaec139e
--- /dev/null
+++ b/modules/nf-core/multiqc/main.nf
@@ -0,0 +1,63 @@
+process MULTIQC {
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }"
+
+    input:
+    path  multiqc_files, stageAs: "?/*"
+    path(multiqc_config)
+    path(extra_multiqc_config)
+    path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
+
+    output:
+    path "*multiqc_report.html", emit: report
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
+    path "versions.yml"        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
+    def config = multiqc_config ? "--config $multiqc_config" : ''
+    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
+    """
+    multiqc \\
+        --force \\
+        $args \\
+        $config \\
+        $prefix \\
+        $extra_config \\
+        $logo \\
+        $replace \\
+        $samples \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir multiqc_data
+    touch multiqc_plots
+    touch multiqc_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
new file mode 100644
index 000000000..382c08cbc
--- /dev/null
+++ b/modules/nf-core/multiqc/meta.yml
@@ -0,0 +1,71 @@
+name: multiqc
+description: Aggregate results from bioinformatics analyses across many samples into a single report
+keywords:
+  - QC
+  - bioinformatics tools
+  - Beautiful stand-alone HTML report
+tools:
+  - multiqc:
+      description: |
+        MultiQC searches a given directory for analysis logs and compiles a HTML report.
+        It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+      homepage: https://multiqc.info/
+      documentation: https://multiqc.info/docs/
+      licence: ["GPL-3.0-or-later"]
+input:
+  - multiqc_files:
+      type: file
+      description: |
+        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
+      pattern: "*.{yml,yaml}"
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+  - replace_names:
+      type: file
+      description: |
+        Optional two-column sample renaming file. First column a set of
+        patterns, second column a set of corresponding replacements. Passed via
+        MultiQC's `--replace-names` option.
+      pattern: "*.{tsv}"
+  - sample_names:
+      type: file
+      description: |
+        Optional TSV file with headers, passed to the MultiQC --sample_names
+        argument.
+      pattern: "*.{tsv}"
+output:
+  - report:
+      type: file
+      description: MultiQC report file
+      pattern: "multiqc_report.html"
+  - data:
+      type: directory
+      description: MultiQC data dir
+      pattern: "multiqc_data"
+  - plots:
+      type: file
+      description: Plots created by MultiQC
+      pattern: "*_data"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@abhi18av"
+  - "@bunop"
+  - "@drpatelh"
+  - "@jfy133"
+maintainers:
+  - "@abhi18av"
+  - "@bunop"
+  - "@drpatelh"
+  - "@jfy133"
diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config
new file mode 100644
index 000000000..ac178787c
--- /dev/null
+++ b/modules/nf-core/multiqc/nextflow.config
@@ -0,0 +1,16 @@
+if (!params.skip_multiqc) {
+    process {
+        withName: 'MULTIQC' {
+            ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+            ext.prefix = "multiqc_report"
+            publishDir = [
+                path: { [
+                    "${params.outdir}/multiqc",
+                    params.skip_alignment? '' : "/${params.aligner}"
+                    ].join('') },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
new file mode 100644
index 000000000..f815b6de3
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test Process MULTIQC"
+    script "../main.nf"
+    process "MULTIQC"
+    config "./nextflow.config"
+
+    test("sarscov2 single-end [fastqc]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("multiqc_versions_single") }
+            )
+        }
+
+    }
+
+    test("sarscov2 single-end [fastqc] [config]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+                input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("multiqc_versions_config") }
+            )
+        }
+    }
+
+    test("sarscov2 single-end [fastqc] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.report.collect { file(it).getName() } +
+                                process.out.data.collect { file(it).getName() } +
+                                process.out.plots.collect { file(it).getName() } +
+                                process.out.versions ).match("multiqc_stub") }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
new file mode 100644
index 000000000..83fa080c8
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -0,0 +1,41 @@
+{
+    "multiqc_versions_single": {
+        "content": [
+            [
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T12:41:34.562023"
+    },
+    "multiqc_stub": {
+        "content": [
+            [
+                "multiqc_report.html",
+                "multiqc_data",
+                "multiqc_plots",
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T11:27:11.933869532"
+    },
+    "multiqc_versions_config": {
+        "content": [
+            [
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T11:26:56.709849369"
+    }
+}
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 000000000..c537a6a3e
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
+}
diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml
new file mode 100644
index 000000000..58b795f54
--- /dev/null
+++ b/modules/nf-core/picard/markduplicates/environment.yml
@@ -0,0 +1,7 @@
+name: picard_markduplicates
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::picard=3.1.1
diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
index ebfa0864d..ad0b29636 100644
--- a/modules/nf-core/picard/markduplicates/main.nf
+++ b/modules/nf-core/picard/markduplicates/main.nf
@@ -2,19 +2,20 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
+        'biocontainers/picard:3.1.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(reads)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
 
     output:
-    tuple val(meta), path("*.bam")        , emit: bam
-    tuple val(meta), path("*.bai")        , optional:true, emit: bai
+    tuple val(meta), path("*.bam") , emit: bam,  optional: true
+    tuple val(meta), path("*.bai") , emit: bai,  optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
     tuple val(meta), path("*.metrics.txt"), emit: metrics
     path  "versions.yml"                  , emit: versions
 
@@ -24,6 +25,8 @@ process PICARD_MARKDUPLICATES {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix    ?: "${reads.getExtension()}"
+    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
     def avail_mem = 3072
     if (!task.memory) {
         log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -31,16 +34,16 @@ process PICARD_MARKDUPLICATES {
         avail_mem = (task.memory.mega*0.8).intValue()
     }
 
-    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
 
     """
     picard \\
         -Xmx${avail_mem}M \\
         MarkDuplicates \\
         $args \\
-        --INPUT $bam \\
-        --OUTPUT ${prefix}.bam \\
-        --REFERENCE_SEQUENCE $fasta \\
+        --INPUT $reads \\
+        --OUTPUT ${prefix}.${suffix} \\
+        $reference \\
         --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
 
     cat <<-END_VERSIONS > versions.yml
@@ -51,10 +54,10 @@ process PICARD_MARKDUPLICATES {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    def suffix = task.ext.suffix    ?: "${reads.getExtension()}"
+    if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
-    touch ${prefix}.bam
-    touch ${prefix}.bam.bai
+    touch ${prefix}.${suffix}
     touch ${prefix}.MarkDuplicates.metrics.txt
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml
index f7693d2f0..1f0ffe16c 100644
--- a/modules/nf-core/picard/markduplicates/meta.yml
+++ b/modules/nf-core/picard/markduplicates/meta.yml
@@ -21,9 +21,9 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - reads:
       type: file
-      description: BAM file
+      description: Sequence reads file, can be SAM/BAM/CRAM format
       pattern: "*.{bam,cram,sam}"
   - meta2:
       type: map
@@ -32,7 +32,7 @@ input:
         e.g. [ id:'genome' ]
   - fasta:
       type: file
-      description: Reference genome fasta file
+      description: Reference genome fasta file, required for CRAM input
       pattern: "*.{fasta,fa}"
   - meta3:
       type: map
@@ -57,6 +57,10 @@ output:
       type: file
       description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag
       pattern: "*.{bai}"
+  - cram:
+      type: file
+      description: Output CRAM file
+      pattern: "*.{cram}"
   - metrics:
       type: file
       description: Duplicate metrics file generated by picard
@@ -69,3 +73,7 @@ authors:
   - "@drpatelh"
   - "@projectoriented"
   - "@ramprasadn"
+maintainers:
+  - "@drpatelh"
+  - "@projectoriented"
+  - "@ramprasadn"
diff --git a/modules/nf-core/picard/markduplicates/picard-markduplicates.diff b/modules/nf-core/picard/markduplicates/picard-markduplicates.diff
new file mode 100644
index 000000000..bf684640d
--- /dev/null
+++ b/modules/nf-core/picard/markduplicates/picard-markduplicates.diff
@@ -0,0 +1,25 @@
+Changes in module 'nf-core/picard/markduplicates'
+--- modules/nf-core/picard/markduplicates/main.nf
++++ modules/nf-core/picard/markduplicates/main.nf
+@@ -4,8 +4,8 @@
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+-        'biocontainers/picard:3.2.0--hdfd78af_0' }"
++        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
++        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+ 
+     input:
+     tuple val(meta), path(reads)
+
+--- modules/nf-core/picard/markduplicates/environment.yml
++++ modules/nf-core/picard/markduplicates/environment.yml
+@@ -4,4 +4,4 @@
+   - bioconda
+   - defaults
+ dependencies:
+-  - bioconda::picard=3.2.0
++  - bioconda::picard=3.1.1
+
+************************************************************
diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test
new file mode 100644
index 000000000..1abea33e3
--- /dev/null
+++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test
@@ -0,0 +1,169 @@
+nextflow_process {
+
+    name "Test Process PICARD_MARKDUPLICATES"
+    script "../main.nf"
+    process "PICARD_MARKDUPLICATES"
+    config "./nextflow.config"
+
+    test("sarscov2 [unsorted bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ])
+                input[1] = [ [:], [] ]
+                input[2] = [ [:], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    path(process.out.metrics.get(0).get(1)).readLines()[0..2],
+                    process.out.versions)
+                .match() }
+            )
+        }
+    }
+
+    test("sarscov2 [sorted bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                input[1] = [ [:], [] ]
+                input[2] = [ [:], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    path(process.out.metrics.get(0).get(1)).readLines()[0..2],
+                    process.out.versions)
+                .match() }
+            )
+        }
+    }
+
+    test("homo_sapiens [cram]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.cram[0][1]).name,
+                    path(process.out.metrics.get(0).get(1)).readLines()[0..2],
+                    process.out.versions)
+                .match() }
+            )
+        }
+    }
+
+    test("sarscov2 [unsorted bam] - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ])
+                input[1] = [ [:], [] ]
+                input[2] = [ [:], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [sorted bam] - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                input[1] = [ [:], [] ]
+                input[2] = [ [:], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens [cram] - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap
new file mode 100644
index 000000000..1a6598aa9
--- /dev/null
+++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap
@@ -0,0 +1,251 @@
+{
+    "sarscov2 [sorted bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+                ],
+                "bai": [
+                    
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "cram": [
+                    
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:34:20.663558"
+    },
+    "sarscov2 [unsorted bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+                ],
+                "bai": [
+                    
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "cram": [
+                    
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:34:01.021052"
+    },
+    "sarscov2 [unsorted bam]": {
+        "content": [
+            "test.marked.bam",
+            [
+                "## htsjdk.samtools.metrics.StringHeader",
+                "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "## htsjdk.samtools.metrics.StringHeader"
+            ],
+            [
+                "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:32:49.777427"
+    },
+    "sarscov2 [sorted bam]": {
+        "content": [
+            "test.marked.bam",
+            [
+                "## htsjdk.samtools.metrics.StringHeader",
+                "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "## htsjdk.samtools.metrics.StringHeader"
+            ],
+            [
+                "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:33:14.462596"
+    },
+    "homo_sapiens [cram]": {
+        "content": [
+            "test.marked.cram",
+            [
+                "## htsjdk.samtools.metrics.StringHeader",
+                "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "## htsjdk.samtools.metrics.StringHeader"
+            ],
+            [
+                "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:33:40.215159"
+    },
+    "homo_sapiens [cram] - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+                ],
+                "bai": [
+                    
+                ],
+                "bam": [
+                    
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:34:51.753515"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/markduplicates/tests/nextflow.config b/modules/nf-core/picard/markduplicates/tests/nextflow.config
new file mode 100644
index 000000000..02818dd6e
--- /dev/null
+++ b/modules/nf-core/picard/markduplicates/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: PICARD_MARKDUPLICATES {
+        ext.prefix = { "${meta.id}.marked" }
+        ext.args = '--ASSUME_SORT_ORDER queryname'
+    }
+}
diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml
new file mode 100644
index 000000000..57b8b9c67
--- /dev/null
+++ b/modules/nf-core/preseq/lcextrap/environment.yml
@@ -0,0 +1,7 @@
+name: preseq_lcextrap
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::preseq=3.1.2
diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf
index 12546f0a2..3fec468e9 100644
--- a/modules/nf-core/preseq/lcextrap/main.nf
+++ b/modules/nf-core/preseq/lcextrap/main.nf
@@ -1,9 +1,9 @@
 process PRESEQ_LCEXTRAP {
     tag "$meta.id"
     label 'process_single'
-    label 'error_ignore'
+    label 'error_retry'
 
-    conda "bioconda::preseq=3.1.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2':
         'biocontainers/preseq:3.1.2--h445547b_2' }"
@@ -21,6 +21,7 @@ process PRESEQ_LCEXTRAP {
 
     script:
     def args = task.ext.args ?: ''
+    args = task.attempt > 1 ? args.join(' -defects') : args  // Disable testing for defects
     def prefix = task.ext.prefix ?: "${meta.id}"
     def paired_end = meta.single_end ? '' : '-pe'
     """
@@ -37,4 +38,16 @@ process PRESEQ_LCEXTRAP {
         preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.lc_extrap.txt
+    touch ${prefix}.command.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/preseq/lcextrap/meta.yml b/modules/nf-core/preseq/lcextrap/meta.yml
old mode 100755
new mode 100644
index 1391961c8..c00fa8eef
--- a/modules/nf-core/preseq/lcextrap/meta.yml
+++ b/modules/nf-core/preseq/lcextrap/meta.yml
@@ -10,9 +10,7 @@ tools:
       homepage: http://smithlabresearch.org/software/preseq/
       documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf
       tool_dev_url: https://github.com/smithlabcode/preseq
-
       licence: ["GPL"]
-
 input:
   - meta:
       type: map
@@ -23,7 +21,6 @@ input:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
-
 output:
   - meta:
       type: map
@@ -42,7 +39,9 @@ output:
       type: file
       description: Log file containing stderr produced by Preseq
       pattern: "*.{log}"
-
 authors:
   - "@drpatelh"
-  - "@Emiller88"
+  - "@edmundmiller"
+maintainers:
+  - "@drpatelh"
+  - "@edmundmiller"
diff --git a/modules/nf-core/preseq/lcextrap/nextflow.config b/modules/nf-core/preseq/lcextrap/nextflow.config
new file mode 100644
index 000000000..e203e87e7
--- /dev/null
+++ b/modules/nf-core/preseq/lcextrap/nextflow.config
@@ -0,0 +1,21 @@
+if (!params.skip_alignment && !params.skip_qc) {
+    if (!params.skip_preseq) {
+        process {
+            withName: 'PRESEQ_LCEXTRAP' {
+                ext.args   = '-verbose -bam -seed 1 -seg_len 100000000'
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/preseq" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*.txt"
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/preseq/log" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*.log"
+                    ]
+                ]
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test b/modules/nf-core/preseq/lcextrap/tests/main.nf.test
new file mode 100644
index 000000000..50e44157e
--- /dev/null
+++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test
@@ -0,0 +1,96 @@
+nextflow_process {
+
+    name "Test Process PRESEQ_LCEXTRAP"
+    script "../main.nf"
+    process "PRESEQ_LCEXTRAP"
+
+    test("sarscov2 - single_end") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.log[0][1]).name).match("single_end - log") },
+                { assert snapshot(process.out.lc_extrap).match("single_end - lc_extrap") },
+                { assert snapshot(process.out.versions).match("single_end - versions") }
+            )
+        }
+    }
+
+    test("sarscov2 - single_end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - paired_end") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.log[0][1]).name).match("paired_end - log") },
+                { assert snapshot(process.out.lc_extrap).match("paired_end - lc_extrap") },
+                { assert snapshot(process.out.versions).match("paired_end - versions") }
+            )
+        }
+    }
+
+    test("sarscov2 - paired_end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap
new file mode 100644
index 000000000..3f95cd498
--- /dev/null
+++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap
@@ -0,0 +1,188 @@
+{
+    "single_end - lc_extrap": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.lc_extrap.txt:md5,1fa5cdd601079329618f61660bee00de"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T17:20:40.735535"
+    },
+    "paired_end - log": {
+        "content": [
+            "test.command.log"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T17:20:51.981746"
+    },
+    "single_end - versions": {
+        "content": [
+            [
+                "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T17:20:40.74601"
+    },
+    "sarscov2 - single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.lc_extrap.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922"
+                ],
+                "lc_extrap": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.lc_extrap.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T18:43:12.689062"
+    },
+    "paired_end - versions": {
+        "content": [
+            [
+                "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T17:20:52.02843"
+    },
+    "single_end - log": {
+        "content": [
+            "test.command.log"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T17:20:40.72985"
+    },
+    "paired_end - lc_extrap": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.lc_extrap.txt:md5,10e5ea860e87fb6f5dc10f4f20c62040"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T17:20:51.998533"
+    },
+    "sarscov2 - paired_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.lc_extrap.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922"
+                ],
+                "lc_extrap": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.lc_extrap.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T18:43:32.569811"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml
new file mode 100644
index 000000000..590ae85f7
--- /dev/null
+++ b/modules/nf-core/qualimap/rnaseq/environment.yml
@@ -0,0 +1,7 @@
+name: qualimap_rnaseq
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::qualimap=2.3
diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf
index b8a370973..4411d8689 100644
--- a/modules/nf-core/qualimap/rnaseq/main.nf
+++ b/modules/nf-core/qualimap/rnaseq/main.nf
@@ -2,7 +2,7 @@ process QUALIMAP_RNASEQ {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::qualimap=2.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/qualimap:2.3--hdfd78af_0' :
         'biocontainers/qualimap:2.3--hdfd78af_0' }"
diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml
index 7738f08d8..6f766e4f5 100644
--- a/modules/nf-core/qualimap/rnaseq/meta.yml
+++ b/modules/nf-core/qualimap/rnaseq/meta.yml
@@ -50,3 +50,5 @@ output:
       pattern: "versions.yml"
 authors:
   - "@FriederikeHanssen"
+maintainers:
+  - "@FriederikeHanssen"
diff --git a/modules/nf-core/qualimap/rnaseq/nextflow.config b/modules/nf-core/qualimap/rnaseq/nextflow.config
new file mode 100644
index 000000000..9c05fb25a
--- /dev/null
+++ b/modules/nf-core/qualimap/rnaseq/nextflow.config
@@ -0,0 +1,13 @@
+if (!params.skip_alignment && !params.skip_qc) {
+    if (!params.skip_qualimap) {
+        process {
+            withName: 'QUALIMAP_RNASEQ' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/qualimap" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+}
diff --git a/modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff b/modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff
deleted file mode 100644
index 48f498081..000000000
--- a/modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/qualimap/rnaseq'
---- modules/nf-core/qualimap/rnaseq/main.nf
-+++ modules/nf-core/qualimap/rnaseq/main.nf
-@@ -2,10 +2,10 @@
-     tag "$meta.id"
-     label 'process_medium'
- 
--    conda "bioconda::qualimap=2.2.2d"
-+    conda "bioconda::qualimap=2.3"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' :
--        'biocontainers/qualimap:2.2.2d--1' }"
-+        'https://depot.galaxyproject.org/singularity/qualimap:2.3--hdfd78af_0' :
-+        'biocontainers/qualimap:2.3--hdfd78af_0' }"
- 
-     input:
-     tuple val(meta), path(bam)
-
-************************************************************
diff --git a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test
new file mode 100644
index 000000000..ff4197eeb
--- /dev/null
+++ b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test
@@ -0,0 +1,61 @@
+nextflow_process {
+
+    name "Test Process QUALIMAP_RNASEQ"
+    script "../main.nf"
+    process "QUALIMAP_RNASEQ"
+
+    test("homo_sapiens [bam]") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'test_fasta_gtf' ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    file("${process.out.results[0][1]}/qualimapReport.html").name,
+                    path("${process.out.results[0][1]}/rnaseq_qc_results.txt"),
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens [bam] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'test_fasta_gtf' ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test.snap b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test.snap
new file mode 100644
index 000000000..682462639
--- /dev/null
+++ b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test.snap
@@ -0,0 +1,55 @@
+{
+    "homo_sapiens [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a6868ab89f7d31361a7791db2dea98e7"
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a6868ab89f7d31361a7791db2dea98e7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:27:41.158111"
+    },
+    "homo_sapiens [bam]": {
+        "content": [
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt:md5,b77878cac45beaa79a892af54aad2da3",
+            [
+                "versions.yml:md5,a6868ab89f7d31361a7791db2dea98e7"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:27:30.782304"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml
new file mode 100644
index 000000000..b811fa6fe
--- /dev/null
+++ b/modules/nf-core/rsem/calculateexpression/environment.yml
@@ -0,0 +1,8 @@
+name: rsem_calculateexpression
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rsem=1.3.3
+  - bioconda::star=2.7.10a
diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf
index 54041aedb..40bddc5e5 100644
--- a/modules/nf-core/rsem/calculateexpression/main.nf
+++ b/modules/nf-core/rsem/calculateexpression/main.nf
@@ -2,7 +2,7 @@ process RSEM_CALCULATEEXPRESSION {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::rsem=1.3.3 bioconda::star=2.7.10a"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
         'biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
@@ -54,4 +54,22 @@ process RSEM_CALCULATEEXPRESSION {
         star: \$(STAR --version | sed -e "s/STAR_//g")
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.genes.results
+    touch ${prefix}.isoforms.results
+    touch ${prefix}.stat
+    touch ${prefix}.log
+    touch ${prefix}.STAR.genome.bam
+    touch ${prefix}.genome.bam
+    touch ${prefix}.transcript.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
+        star: \$(STAR --version | sed -e "s/STAR_//g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/rsem/calculateexpression/meta.yml b/modules/nf-core/rsem/calculateexpression/meta.yml
index 680ede2e2..e6d580e9b 100644
--- a/modules/nf-core/rsem/calculateexpression/meta.yml
+++ b/modules/nf-core/rsem/calculateexpression/meta.yml
@@ -62,3 +62,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test
new file mode 100644
index 000000000..7af876dd8
--- /dev/null
+++ b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test
@@ -0,0 +1,88 @@
+nextflow_process {
+
+    name "Test Process RSEM_CALCULATEEXPRESSION"
+    script "../main.nf"
+    process "RSEM_CALCULATEEXPRESSION"
+    config "./nextflow.config"
+
+    test("homo_sapiens") {
+
+        setup {
+            run("RSEM_PREPAREREFERENCE") {
+                script "../../../rsem/preparereference/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                    input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true))
+                    """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', strandedness: 'forward' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = RSEM_PREPAREREFERENCE.out.index
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.counts_gene).match("counts_gene") },
+                { assert snapshot(process.out.counts_transcript).match("counts_transcript") },
+                { assert snapshot(process.out.stat).match("stat") },
+                { assert path(process.out.logs.get(0).get(1)).exists() },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("homo_sapiens - stub") {
+
+    options "-stub"
+
+        setup {
+            run("RSEM_PREPAREREFERENCE") {
+                script "../../../rsem/preparereference/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                    input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true))
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', strandedness: 'forward' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = RSEM_PREPAREREFERENCE.out.index
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test.snap b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test.snap
new file mode 100644
index 000000000..61647071d
--- /dev/null
+++ b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test.snap
@@ -0,0 +1,215 @@
+{
+    "stat": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    [
+                        "test.cnt:md5,76249e6b2f3c104f414aae596ba2c2f4",
+                        "test.model:md5,a7a4bc1734918ef5848604e3362b83e2",
+                        "test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-22T13:14:18.68683"
+    },
+    "homo_sapiens - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,823e53afe1ff4f3930ae8392f9f8dd5c"
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_genome": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_star": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_transcript": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_gene": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_transcript": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "logs": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stat": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,823e53afe1ff4f3930ae8392f9f8dd5c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:04:38.064594"
+    },
+    "counts_transcript": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-22T13:14:18.682898"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,823e53afe1ff4f3930ae8392f9f8dd5c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-22T13:14:18.700958"
+    },
+    "counts_gene": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.genes.results:md5,c7ec226f76736ea805771e73553ae359"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-22T13:14:18.670998"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/rsem/calculateexpression/tests/nextflow.config b/modules/nf-core/rsem/calculateexpression/tests/nextflow.config
new file mode 100644
index 000000000..b17a1cf2e
--- /dev/null
+++ b/modules/nf-core/rsem/calculateexpression/tests/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: RSEM_PREPAREREFERENCE {
+        ext.args = '--star'
+    }
+
+    withName: RSEM_CALCULATEEXPRESSION {
+        ext.args = '--star --star-gzipped-read-file'
+    }
+
+}
diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml
new file mode 100644
index 000000000..c80e69106
--- /dev/null
+++ b/modules/nf-core/rsem/preparereference/environment.yml
@@ -0,0 +1,8 @@
+name: rsem_preparereference
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rsem=1.3.3
+  - bioconda::star=2.7.10a
diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf
index 62b93d08a..1acfbdedb 100644
--- a/modules/nf-core/rsem/preparereference/main.nf
+++ b/modules/nf-core/rsem/preparereference/main.nf
@@ -2,7 +2,7 @@ process RSEM_PREPAREREFERENCE {
     tag "$fasta"
     label 'process_high'
 
-    conda "bioconda::rsem=1.3.3 bioconda::star=2.7.10a"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
         'biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
@@ -69,4 +69,15 @@ process RSEM_PREPAREREFERENCE {
         END_VERSIONS
         """
     }
+
+    stub:
+    """
+    touch genome.transcripts.fa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
+        star: \$(STAR --version | sed -e "s/STAR_//g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/rsem/preparereference/meta.yml b/modules/nf-core/rsem/preparereference/meta.yml
index 3568e1911..05aa44fe6 100644
--- a/modules/nf-core/rsem/preparereference/meta.yml
+++ b/modules/nf-core/rsem/preparereference/meta.yml
@@ -37,3 +37,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/rsem/preparereference/tests/main.nf.test b/modules/nf-core/rsem/preparereference/tests/main.nf.test
new file mode 100644
index 000000000..210e03e87
--- /dev/null
+++ b/modules/nf-core/rsem/preparereference/tests/main.nf.test
@@ -0,0 +1,51 @@
+nextflow_process {
+
+    name "Test Process RSEM_PREPAREREFERENCE"
+    script "../main.nf"
+    process "RSEM_PREPAREREFERENCE"
+
+    test("homo_sapiens") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.index).match("index")},
+                { assert snapshot(process.out.transcript_fasta).match("transcript_fasta")},
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("homo_sapiens - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/rsem/preparereference/tests/main.nf.test.snap b/modules/nf-core/rsem/preparereference/tests/main.nf.test.snap
new file mode 100644
index 000000000..667416bff
--- /dev/null
+++ b/modules/nf-core/rsem/preparereference/tests/main.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "homo_sapiens - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "genome.fasta:md5,f315020d899597c1b57e5fe9f60f4c3e"
+                    ]
+                ],
+                "1": [
+                    "genome.transcripts.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "versions.yml:md5,517611c42f6354d3609db1b35fffa397"
+                ],
+                "index": [
+                    [
+                        "genome.fasta:md5,f315020d899597c1b57e5fe9f60f4c3e"
+                    ]
+                ],
+                "transcript_fasta": [
+                    "genome.transcripts.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,517611c42f6354d3609db1b35fffa397"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:00:50.389847"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,517611c42f6354d3609db1b35fffa397"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-22T13:16:49.170587"
+    },
+    "index": {
+        "content": [
+            [
+                [
+                    "genome.chrlist:md5,b190587cae0531f3cf25552d8aa674db",
+                    "genome.fasta:md5,f315020d899597c1b57e5fe9f60f4c3e",
+                    "genome.grp:md5,c2848a8b6d495956c11ec53efc1de67e",
+                    "genome.idx.fa:md5,050c521a2719c2ae48267c1e65218f29",
+                    "genome.n2g.idx.fa:md5,050c521a2719c2ae48267c1e65218f29",
+                    "genome.seq:md5,94da0c6b88c33e63c9a052a11f4f57c1",
+                    "genome.ti:md5,c9e4ae8d4d13a504eec2acf1b8589a66",
+                    "genome.transcripts.fa:md5,050c521a2719c2ae48267c1e65218f29"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-22T13:16:49.140398"
+    },
+    "transcript_fasta": {
+        "content": [
+            [
+                "genome.transcripts.fa:md5,050c521a2719c2ae48267c1e65218f29"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-22T13:16:49.159946"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml
new file mode 100644
index 000000000..e960c9943
--- /dev/null
+++ b/modules/nf-core/rseqc/bamstat/environment.yml
@@ -0,0 +1,8 @@
+name: rseqc_bamstat
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rseqc=5.0.3
+  - conda-forge::r-base>=3.5
diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf
index 66c9a7451..167240c46 100644
--- a/modules/nf-core/rseqc/bamstat/main.nf
+++ b/modules/nf-core/rseqc/bamstat/main.nf
@@ -2,7 +2,7 @@ process RSEQC_BAMSTAT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::rseqc=5.0.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
         'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
@@ -31,4 +31,15 @@ process RSEQC_BAMSTAT {
         rseqc: \$(bam_stat.py --version | sed -e "s/bam_stat.py //g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam_stat.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rseqc: \$(bam_stat.py --version | sed -e "s/bam_stat.py //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/rseqc/bamstat/meta.yml b/modules/nf-core/rseqc/bamstat/meta.yml
index 2d7fa7996..72745310c 100644
--- a/modules/nf-core/rseqc/bamstat/meta.yml
+++ b/modules/nf-core/rseqc/bamstat/meta.yml
@@ -35,3 +35,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/rseqc/bamstat/rseqc-bamstat.diff b/modules/nf-core/rseqc/bamstat/rseqc-bamstat.diff
deleted file mode 100644
index a8ee45a91..000000000
--- a/modules/nf-core/rseqc/bamstat/rseqc-bamstat.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/rseqc/bamstat'
---- modules/nf-core/rseqc/bamstat/main.nf
-+++ modules/nf-core/rseqc/bamstat/main.nf
-@@ -2,10 +2,10 @@
-     tag "$meta.id"
-     label 'process_medium'
- 
--    conda "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'"
-+    conda "bioconda::rseqc=5.0.3"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
--        'biocontainers/rseqc:3.0.1--py37h516909a_1' }"
-+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-+        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
- 
-     input:
-     tuple val(meta), path(bam)
-
-************************************************************
diff --git a/modules/nf-core/rseqc/bamstat/tests/main.nf.test b/modules/nf-core/rseqc/bamstat/tests/main.nf.test
new file mode 100644
index 000000000..fd6fc0811
--- /dev/null
+++ b/modules/nf-core/rseqc/bamstat/tests/main.nf.test
@@ -0,0 +1,47 @@
+nextflow_process {
+
+    name "Test Process RSEQC_BAMSTAT"
+    script "../main.nf"
+    process "RSEQC_BAMSTAT"
+    config "./nextflow.config"
+
+    test("sarscov2 - [meta] - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam')
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+    test("sarscov2 - [meta] - bam - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam')
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+}
diff --git a/modules/nf-core/rseqc/bamstat/tests/main.nf.test.snap b/modules/nf-core/rseqc/bamstat/tests/main.nf.test.snap
new file mode 100644
index 000000000..deae0e80d
--- /dev/null
+++ b/modules/nf-core/rseqc/bamstat/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "sarscov2 - [meta] - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam_stat.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,58f74a7ff9d2966142c81a4a4735dbf3"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam_stat.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,58f74a7ff9d2966142c81a4a4735dbf3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:16:13.970299"
+    },
+    "sarscov2 - [meta] - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam_stat.txt:md5,2675857864c1d1139b2a19d25dc36b09"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,58f74a7ff9d2966142c81a4a4735dbf3"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam_stat.txt:md5,2675857864c1d1139b2a19d25dc36b09"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,58f74a7ff9d2966142c81a4a4735dbf3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2023-12-14T17:00:23.830276754"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kallisto/quant/tests/paired_end.config b/modules/nf-core/rseqc/bamstat/tests/nextflow.config
similarity index 100%
rename from modules/nf-core/kallisto/quant/tests/paired_end.config
rename to modules/nf-core/rseqc/bamstat/tests/nextflow.config
diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml
new file mode 100644
index 000000000..78215985a
--- /dev/null
+++ b/modules/nf-core/rseqc/inferexperiment/environment.yml
@@ -0,0 +1,8 @@
+name: rseqc_inferexperiment
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rseqc=5.0.3
+  - conda-forge::r-base>=3.5
diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf
index df24d7262..87c676ada 100644
--- a/modules/nf-core/rseqc/inferexperiment/main.nf
+++ b/modules/nf-core/rseqc/inferexperiment/main.nf
@@ -2,7 +2,7 @@ process RSEQC_INFEREXPERIMENT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::rseqc=5.0.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
         'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
@@ -33,4 +33,15 @@ process RSEQC_INFEREXPERIMENT {
         rseqc: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.infer_experiment.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rseqc: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/rseqc/inferexperiment/meta.yml b/modules/nf-core/rseqc/inferexperiment/meta.yml
index b4162059d..d9b9ff63e 100644
--- a/modules/nf-core/rseqc/inferexperiment/meta.yml
+++ b/modules/nf-core/rseqc/inferexperiment/meta.yml
@@ -2,6 +2,7 @@ name: rseqc_inferexperiment
 description: Infer strandedness from sequencing reads
 keywords:
   - rnaseq
+  - strandedness
   - experiment
 tools:
   - rseqc:
@@ -38,3 +39,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/rseqc/inferexperiment/rseqc-inferexperiment.diff b/modules/nf-core/rseqc/inferexperiment/rseqc-inferexperiment.diff
deleted file mode 100644
index 728b4799f..000000000
--- a/modules/nf-core/rseqc/inferexperiment/rseqc-inferexperiment.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/rseqc/inferexperiment'
---- modules/nf-core/rseqc/inferexperiment/main.nf
-+++ modules/nf-core/rseqc/inferexperiment/main.nf
-@@ -2,10 +2,10 @@
-     tag "$meta.id"
-     label 'process_medium'
- 
--    conda "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'"
-+    conda "bioconda::rseqc=5.0.3"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
--        'biocontainers/rseqc:3.0.1--py37h516909a_1' }"
-+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-+        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
- 
-     input:
-     tuple val(meta), path(bam)
-
-************************************************************
diff --git a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test
new file mode 100644
index 000000000..375f65357
--- /dev/null
+++ b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test
@@ -0,0 +1,49 @@
+nextflow_process {
+
+    name "Test Process RSEQC_INFEREXPERIMENT"
+    script "../main.nf"
+    process "RSEQC_INFEREXPERIMENT"
+    config "./nextflow.config"
+
+    test("sarscov2 - [[meta] - bam] - bed") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+    test("sarscov2 - [[meta] - bam] - bed - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+}
diff --git a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test.snap b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test.snap
new file mode 100644
index 000000000..e31c1129f
--- /dev/null
+++ b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "sarscov2 - [[meta] - bam] - bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.infer_experiment.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f56ba5c6208ae720dd730f3a432e3ba7"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.infer_experiment.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f56ba5c6208ae720dd730f3a432e3ba7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:34:31.050305"
+    },
+    "sarscov2 - [[meta] - bam] - bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.infer_experiment.txt:md5,f9d0bfc239df637cd8aeda40ade3c59a"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f56ba5c6208ae720dd730f3a432e3ba7"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.infer_experiment.txt:md5,f9d0bfc239df637cd8aeda40ade3c59a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f56ba5c6208ae720dd730f3a432e3ba7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:33:19.853327"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kallisto/quant/tests/single_end.config b/modules/nf-core/rseqc/inferexperiment/tests/nextflow.config
similarity index 92%
rename from modules/nf-core/kallisto/quant/tests/single_end.config
rename to modules/nf-core/rseqc/inferexperiment/tests/nextflow.config
index 7022246bc..8730f1c4b 100644
--- a/modules/nf-core/kallisto/quant/tests/single_end.config
+++ b/modules/nf-core/rseqc/inferexperiment/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
-    
+
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
+
 }
diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml
new file mode 100644
index 000000000..fb6e9e925
--- /dev/null
+++ b/modules/nf-core/rseqc/innerdistance/environment.yml
@@ -0,0 +1,8 @@
+name: rseqc_innerdistance
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rseqc=5.0.3
+  - conda-forge::r-base>=3.5
diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf
index b84115cee..207f5fb4d 100644
--- a/modules/nf-core/rseqc/innerdistance/main.nf
+++ b/modules/nf-core/rseqc/innerdistance/main.nf
@@ -2,7 +2,7 @@ process RSEQC_INNERDISTANCE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::rseqc=5.0.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
         'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
@@ -48,4 +48,19 @@ process RSEQC_INNERDISTANCE {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.inner_distance.txt
+    touch ${prefix}.inner_distance_freq.txt
+    touch ${prefix}.inner_distance_mean.txt
+    touch ${prefix}.inner_distance_plot.pdf
+    touch ${prefix}.inner_distance_plot.r
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rseqc: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/rseqc/innerdistance/meta.yml b/modules/nf-core/rseqc/innerdistance/meta.yml
index d10a4c445..d0a5bf181 100644
--- a/modules/nf-core/rseqc/innerdistance/meta.yml
+++ b/modules/nf-core/rseqc/innerdistance/meta.yml
@@ -1,6 +1,7 @@
 name: rseqc_innerdistance
 description: Calculate inner distance between read pairs.
 keywords:
+  - read_pairs
   - fragment_size
   - inner_distance
 tools:
@@ -54,3 +55,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/rseqc/innerdistance/rseqc-innerdistance.diff b/modules/nf-core/rseqc/innerdistance/rseqc-innerdistance.diff
deleted file mode 100644
index dc760c5da..000000000
--- a/modules/nf-core/rseqc/innerdistance/rseqc-innerdistance.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/rseqc/innerdistance'
---- modules/nf-core/rseqc/innerdistance/main.nf
-+++ modules/nf-core/rseqc/innerdistance/main.nf
-@@ -2,10 +2,10 @@
-     tag "$meta.id"
-     label 'process_medium'
- 
--    conda "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'"
-+    conda "bioconda::rseqc=5.0.3"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
--        'biocontainers/rseqc:3.0.1--py37h516909a_1' }"
-+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-+        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
- 
-     input:
-     tuple val(meta), path(bam)
-
-************************************************************
diff --git a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test
new file mode 100644
index 000000000..e54036f8a
--- /dev/null
+++ b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test
@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process RSEQC_INNERDISTANCE"
+    script "../main.nf"
+    process "RSEQC_INNERDISTANCE"
+    config "./nextflow.config"
+
+    test("sarscov2 - [[meta] - bam] - bed") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.pdf[0][1]).name).match("pdf") },
+                { assert snapshot(process.out.distance).match("distance") },
+                { assert snapshot(process.out.freq).match("freq") },
+                { assert snapshot(process.out.freq).match("rscript") },
+                { assert snapshot(process.out.mean).match("mean") },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 - [[meta] - bam] - bed - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test.snap b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test.snap
new file mode 100644
index 000000000..83f33363a
--- /dev/null
+++ b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test.snap
@@ -0,0 +1,189 @@
+{
+    "rscript": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.inner_distance_freq.txt:md5,3fc037501f5899b5da009c8ce02fc25e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:33:42.467401"
+    },
+    "pdf": {
+        "content": [
+            "test.inner_distance_plot.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:33:42.461959"
+    },
+    "distance": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.inner_distance.txt:md5,a1acc9def0f64a5500d4c4cb47cbe32b"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:33:42.463083"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,3ca19644c7f02a53db3ffe50c7706797"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:33:42.474576"
+    },
+    "mean": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.inner_distance_mean.txt:md5,58398b7d5a29a5e564f9e3c50b55996c"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:33:42.470638"
+    },
+    "sarscov2 - [[meta] - bam] - bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_mean.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,3ca19644c7f02a53db3ffe50c7706797"
+                ],
+                "distance": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "freq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "mean": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_mean.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pdf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "rscript": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3ca19644c7f02a53db3ffe50c7706797"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:22:20.844642"
+    },
+    "freq": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.inner_distance_freq.txt:md5,3fc037501f5899b5da009c8ce02fc25e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:33:42.464983"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/rseqc/innerdistance/tests/nextflow.config b/modules/nf-core/rseqc/innerdistance/tests/nextflow.config
new file mode 100644
index 000000000..8730f1c4b
--- /dev/null
+++ b/modules/nf-core/rseqc/innerdistance/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml
new file mode 100644
index 000000000..35276b715
--- /dev/null
+++ b/modules/nf-core/rseqc/junctionannotation/environment.yml
@@ -0,0 +1,8 @@
+name: rseqc_junctionannotation
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rseqc=5.0.3
+  - conda-forge::r-base>=3.5
diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf
index 9f9c96725..9a8a4653a 100644
--- a/modules/nf-core/rseqc/junctionannotation/main.nf
+++ b/modules/nf-core/rseqc/junctionannotation/main.nf
@@ -2,7 +2,7 @@ process RSEQC_JUNCTIONANNOTATION {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::rseqc=5.0.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
         'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
@@ -33,7 +33,24 @@ process RSEQC_JUNCTIONANNOTATION {
         -r $bed \\
         -o $prefix \\
         $args \\
-        2> ${prefix}.junction_annotation.log
+        2> >(grep -v 'E::idx_find_and_load' | tee ${prefix}.junction_annotation.log >&2)
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rseqc: \$(junction_annotation.py --version | sed -e "s/junction_annotation.py //g")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.junction.xls
+    touch ${prefix}.junction_plot.r
+    touch ${prefix}.junction_annotation.log
+    touch ${prefix}.junction.bed
+    touch ${prefix}.Interact.bed
+    touch ${prefix}.junction.pdf
+    touch ${prefix}.events.pdf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/rseqc/junctionannotation/meta.yml b/modules/nf-core/rseqc/junctionannotation/meta.yml
index 48c43260e..a88aa2db3 100644
--- a/modules/nf-core/rseqc/junctionannotation/meta.yml
+++ b/modules/nf-core/rseqc/junctionannotation/meta.yml
@@ -63,3 +63,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/rseqc/junctionannotation/rseqc-junctionannotation.diff b/modules/nf-core/rseqc/junctionannotation/rseqc-junctionannotation.diff
deleted file mode 100644
index b210db990..000000000
--- a/modules/nf-core/rseqc/junctionannotation/rseqc-junctionannotation.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/rseqc/junctionannotation'
---- modules/nf-core/rseqc/junctionannotation/main.nf
-+++ modules/nf-core/rseqc/junctionannotation/main.nf
-@@ -2,10 +2,10 @@
-     tag "$meta.id"
-     label 'process_medium'
- 
--    conda "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'"
-+    conda "bioconda::rseqc=5.0.3"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
--        'biocontainers/rseqc:3.0.1--py37h516909a_1' }"
-+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-+        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
- 
-     input:
-     tuple val(meta), path(bam)
-
-************************************************************
diff --git a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test
new file mode 100644
index 000000000..8a05bccab
--- /dev/null
+++ b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test
@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process RSEQC_JUNCTIONANNOTATION"
+    script "../main.nf"
+    process "RSEQC_JUNCTIONANNOTATION"
+
+    test("sarscov2 - paired end [bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.rscript.get(0).get(1) ==~ ".*/test.junction_plot.r" },
+                { assert process.out.xls.get(0).get(1) ==~ ".*/test.junction.xls" },
+                { assert snapshot(process.out.log).match("log") },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 - paired end [bam] - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test.snap b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test.snap
new file mode 100644
index 000000000..e87594f0b
--- /dev/null
+++ b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test.snap
@@ -0,0 +1,175 @@
+{
+    "log": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.junction_annotation.log:md5,ef37d06d169a1adbeec23fddf82aee2b"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:32:52.732937"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,091865c0ebd6de262c9b0968b5771091"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:32:52.734515"
+    },
+    "sarscov2 - paired end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction_annotation.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Interact.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.events.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    "versions.yml:md5,091865c0ebd6de262c9b0968b5771091"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "events_pdf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.events.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "interact_bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Interact.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction_annotation.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pdf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "rscript": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,091865c0ebd6de262c9b0968b5771091"
+                ],
+                "xls": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junction.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:39:10.213511"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml
new file mode 100644
index 000000000..7b9cc4fa7
--- /dev/null
+++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml
@@ -0,0 +1,8 @@
+name: rseqc_junctionsaturation
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rseqc=5.0.3
+  - conda-forge::r-base>=3.5
diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf
index f99049c0d..18f063f38 100644
--- a/modules/nf-core/rseqc/junctionsaturation/main.nf
+++ b/modules/nf-core/rseqc/junctionsaturation/main.nf
@@ -2,7 +2,7 @@ process RSEQC_JUNCTIONSATURATION {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::rseqc=5.0.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
         'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
@@ -34,4 +34,16 @@ process RSEQC_JUNCTIONSATURATION {
         rseqc: \$(junction_saturation.py --version | sed -e "s/junction_saturation.py //g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.junctionSaturation_plot.pdf
+    touch ${prefix}.junctionSaturation_plot.r
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rseqc: \$(junction_saturation.py --version | sed -e "s/junction_saturation.py //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/rseqc/junctionsaturation/meta.yml b/modules/nf-core/rseqc/junctionsaturation/meta.yml
index 340fec0d0..19ae3f52d 100644
--- a/modules/nf-core/rseqc/junctionsaturation/meta.yml
+++ b/modules/nf-core/rseqc/junctionsaturation/meta.yml
@@ -43,3 +43,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/rseqc/junctionsaturation/rseqc-junctionsaturation.diff b/modules/nf-core/rseqc/junctionsaturation/rseqc-junctionsaturation.diff
deleted file mode 100644
index 663340cf6..000000000
--- a/modules/nf-core/rseqc/junctionsaturation/rseqc-junctionsaturation.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/rseqc/junctionsaturation'
---- modules/nf-core/rseqc/junctionsaturation/main.nf
-+++ modules/nf-core/rseqc/junctionsaturation/main.nf
-@@ -2,10 +2,10 @@
-     tag "$meta.id"
-     label 'process_medium'
- 
--    conda "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'"
-+    conda "bioconda::rseqc=5.0.3"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
--        'biocontainers/rseqc:3.0.1--py37h516909a_1' }"
-+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-+        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
- 
-     input:
-     tuple val(meta), path(bam)
-
-************************************************************
diff --git a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test
new file mode 100644
index 000000000..69d7f0c5d
--- /dev/null
+++ b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test
@@ -0,0 +1,54 @@
+nextflow_process {
+
+    name "Test Process RSEQC_JUNCTIONSATURATION"
+    script "../main.nf"
+    process "RSEQC_JUNCTIONSATURATION"
+
+    test("sarscov2 paired-end [bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                            [ id:'test', single_end: false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.pdf[0][1]).name).match("pdf") },
+                { assert snapshot(process.out.rscript).match("rscript") },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                            [ id:'test', single_end: false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test.snap b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test.snap
new file mode 100644
index 000000000..8d702a4ef
--- /dev/null
+++ b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test.snap
@@ -0,0 +1,95 @@
+{
+    "rscript": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.junctionSaturation_plot.r:md5,caa6e63dcb477aabb169882b2f30dadd"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:32:24.018924"
+    },
+    "pdf": {
+        "content": [
+            "test.junctionSaturation_plot.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:32:24.011942"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,cd4638541a825dbd44e3cb65d2980aa1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:32:24.021984"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junctionSaturation_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junctionSaturation_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cd4638541a825dbd44e3cb65d2980aa1"
+                ],
+                "pdf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junctionSaturation_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "rscript": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junctionSaturation_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cd4638541a825dbd44e3cb65d2980aa1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:43:55.853893"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml
new file mode 100644
index 000000000..59be9fa88
--- /dev/null
+++ b/modules/nf-core/rseqc/readdistribution/environment.yml
@@ -0,0 +1,8 @@
+name: rseqc_readdistribution
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rseqc=5.0.3
+  - conda-forge::r-base>=3.5
diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf
index 3bf42d1e3..1d9406491 100644
--- a/modules/nf-core/rseqc/readdistribution/main.nf
+++ b/modules/nf-core/rseqc/readdistribution/main.nf
@@ -2,7 +2,7 @@ process RSEQC_READDISTRIBUTION {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::rseqc=5.0.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
         'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
@@ -32,4 +32,15 @@ process RSEQC_READDISTRIBUTION {
         rseqc: \$(read_distribution.py --version | sed -e "s/read_distribution.py //g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.read_distribution.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rseqc: \$(read_distribution.py --version | sed -e "s/read_distribution.py //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/rseqc/readdistribution/meta.yml b/modules/nf-core/rseqc/readdistribution/meta.yml
index 94c647120..989792faa 100644
--- a/modules/nf-core/rseqc/readdistribution/meta.yml
+++ b/modules/nf-core/rseqc/readdistribution/meta.yml
@@ -39,3 +39,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/rseqc/readdistribution/rseqc-readdistribution.diff b/modules/nf-core/rseqc/readdistribution/rseqc-readdistribution.diff
deleted file mode 100644
index 4219e2ac3..000000000
--- a/modules/nf-core/rseqc/readdistribution/rseqc-readdistribution.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/rseqc/readdistribution'
---- modules/nf-core/rseqc/readdistribution/main.nf
-+++ modules/nf-core/rseqc/readdistribution/main.nf
-@@ -2,10 +2,10 @@
-     tag "$meta.id"
-     label 'process_medium'
- 
--    conda "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'"
-+    conda "bioconda::rseqc=5.0.3"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
--        'biocontainers/rseqc:3.0.1--py37h516909a_1' }"
-+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-+        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
- 
-     input:
-     tuple val(meta), path(bam)
-
-************************************************************
diff --git a/modules/nf-core/rseqc/readdistribution/tests/main.nf.test b/modules/nf-core/rseqc/readdistribution/tests/main.nf.test
new file mode 100644
index 000000000..c49c558de
--- /dev/null
+++ b/modules/nf-core/rseqc/readdistribution/tests/main.nf.test
@@ -0,0 +1,52 @@
+nextflow_process {
+
+    name "Test Process RSEQC_READDISTRIBUTION"
+    script "../main.nf"
+    process "RSEQC_READDISTRIBUTION"
+
+    test("sarscov2 paired-end [bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/rseqc/readdistribution/tests/main.nf.test.snap b/modules/nf-core/rseqc/readdistribution/tests/main.nf.test.snap
new file mode 100644
index 000000000..02e5e6117
--- /dev/null
+++ b/modules/nf-core/rseqc/readdistribution/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "sarscov2 paired-end [bam]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.read_distribution.txt:md5,56893fdc0809d968629a363551a1655f"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,fc68a268ab32a0d72a66f270d6c7925e"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.read_distribution.txt:md5,56893fdc0809d968629a363551a1655f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,fc68a268ab32a0d72a66f270d6c7925e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T15:38:36.441841"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.read_distribution.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,fc68a268ab32a0d72a66f270d6c7925e"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.read_distribution.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,fc68a268ab32a0d72a66f270d6c7925e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:50:29.345905"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml
new file mode 100644
index 000000000..c99f107a1
--- /dev/null
+++ b/modules/nf-core/rseqc/readduplication/environment.yml
@@ -0,0 +1,8 @@
+name: rseqc_readduplication
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rseqc=5.0.3
+  - conda-forge::r-base>=3.5
diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf
index d83547205..354338021 100644
--- a/modules/nf-core/rseqc/readduplication/main.nf
+++ b/modules/nf-core/rseqc/readduplication/main.nf
@@ -2,7 +2,7 @@ process RSEQC_READDUPLICATION {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::rseqc=5.0.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
         'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
@@ -34,4 +34,18 @@ process RSEQC_READDUPLICATION {
         rseqc: \$(read_duplication.py --version | sed -e "s/read_duplication.py //g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.seq.DupRate.xls
+    touch ${prefix}.pos.DupRate.xls
+    touch ${prefix}.DupRate_plot.pdf
+    touch ${prefix}.DupRate_plot.r
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rseqc: \$(read_duplication.py --version | sed -e "s/read_duplication.py //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/rseqc/readduplication/meta.yml b/modules/nf-core/rseqc/readduplication/meta.yml
index 5a8666435..4b24d3032 100644
--- a/modules/nf-core/rseqc/readduplication/meta.yml
+++ b/modules/nf-core/rseqc/readduplication/meta.yml
@@ -3,6 +3,8 @@ description: Calculate read duplication rate
 keywords:
   - rnaseq
   - duplication
+  - sequence-based
+  - mapping-based
 tools:
   - rseqc:
       description: |
@@ -50,3 +52,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/rseqc/readduplication/rseqc-readduplication.diff b/modules/nf-core/rseqc/readduplication/rseqc-readduplication.diff
deleted file mode 100644
index 748685c0b..000000000
--- a/modules/nf-core/rseqc/readduplication/rseqc-readduplication.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/rseqc/readduplication'
---- modules/nf-core/rseqc/readduplication/main.nf
-+++ modules/nf-core/rseqc/readduplication/main.nf
-@@ -2,10 +2,10 @@
-     tag "$meta.id"
-     label 'process_medium'
- 
--    conda "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'"
-+    conda "bioconda::rseqc=5.0.3"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
--        'biocontainers/rseqc:3.0.1--py37h516909a_1' }"
-+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-+        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
- 
-     input:
-     tuple val(meta), path(bam)
-
-************************************************************
diff --git a/modules/nf-core/rseqc/readduplication/tests/main.nf.test b/modules/nf-core/rseqc/readduplication/tests/main.nf.test
new file mode 100644
index 000000000..a6ffced4c
--- /dev/null
+++ b/modules/nf-core/rseqc/readduplication/tests/main.nf.test
@@ -0,0 +1,54 @@
+nextflow_process {
+
+    name "Test Process RSEQC_READDUPLICATION"
+    script "../main.nf"
+    process "RSEQC_READDUPLICATION"
+
+    test("sarscov2 paired-end [bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.pdf[0][1]).name).match("pdf") },
+                { assert snapshot(process.out.pos_xls).match("pos_xls") },
+                { assert snapshot(process.out.rscript).match("rscript") },
+                { assert snapshot(process.out.seq_xls).match("seq_xls") },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/rseqc/readduplication/tests/main.nf.test.snap b/modules/nf-core/rseqc/readduplication/tests/main.nf.test.snap
new file mode 100644
index 000000000..143a29dc6
--- /dev/null
+++ b/modules/nf-core/rseqc/readduplication/tests/main.nf.test.snap
@@ -0,0 +1,167 @@
+{
+    "pos_xls": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.pos.DupRate.xls:md5,a859bc2031d46bf1cc4336205847caa3"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T15:43:14.989834"
+    },
+    "rscript": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.DupRate_plot.r:md5,3c0325095cee4835b921e57d61c23dca"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T15:43:15.045525"
+    },
+    "pdf": {
+        "content": [
+            "test.DupRate_plot.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:33:06.857254"
+    },
+    "seq_xls": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.seq.DupRate.xls:md5,ee8783399eec5a18522a6f08bece338b"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T15:43:15.101953"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,8a0721f3247f97135eadb8eecbe142a1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:33:06.877127"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.seq.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.pos.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.DupRate_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.DupRate_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,8a0721f3247f97135eadb8eecbe142a1"
+                ],
+                "pdf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.DupRate_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pos_xls": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.pos.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "rscript": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.DupRate_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "seq_xls": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.seq.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8a0721f3247f97135eadb8eecbe142a1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:53:03.817194"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml
new file mode 100644
index 000000000..288da4300
--- /dev/null
+++ b/modules/nf-core/rseqc/tin/environment.yml
@@ -0,0 +1,8 @@
+name: rseqc_tin
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rseqc=5.0.3
+  - conda-forge::r-base>=3.5
diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf
index 38f1c1757..397442f03 100644
--- a/modules/nf-core/rseqc/tin/main.nf
+++ b/modules/nf-core/rseqc/tin/main.nf
@@ -2,7 +2,7 @@ process RSEQC_TIN {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::rseqc=5.0.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
         'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
@@ -33,4 +33,16 @@ process RSEQC_TIN {
         rseqc: \$(tin.py --version | sed -e "s/tin.py //g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${bam.fileName}.summary.txt
+    touch ${bam.fileName}.tin.xls
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rseqc: \$(tin.py --version | sed -e "s/tin.py //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/rseqc/tin/meta.yml b/modules/nf-core/rseqc/tin/meta.yml
index 381edfde0..f760bb2f4 100644
--- a/modules/nf-core/rseqc/tin/meta.yml
+++ b/modules/nf-core/rseqc/tin/meta.yml
@@ -46,3 +46,5 @@ output:
       pattern: "versions.yml"
 authors:
   - "@drpatelh"
+maintainers:
+  - "@drpatelh"
diff --git a/modules/nf-core/rseqc/tin/rseqc-tin.diff b/modules/nf-core/rseqc/tin/rseqc-tin.diff
deleted file mode 100644
index aa4727128..000000000
--- a/modules/nf-core/rseqc/tin/rseqc-tin.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/rseqc/tin'
---- modules/nf-core/rseqc/tin/main.nf
-+++ modules/nf-core/rseqc/tin/main.nf
-@@ -2,10 +2,10 @@
-     tag "$meta.id"
-     label 'process_high'
- 
--    conda "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'"
-+    conda "bioconda::rseqc=5.0.3"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
--        'biocontainers/rseqc:3.0.1--py37h516909a_1' }"
-+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0' :
-+        'biocontainers/rseqc:5.0.3--py39hf95cd2a_0' }"
- 
-     input:
-     tuple val(meta), path(bam), path(bai)
-
-************************************************************
diff --git a/modules/nf-core/rseqc/tin/tests/main.nf.test b/modules/nf-core/rseqc/tin/tests/main.nf.test
new file mode 100644
index 000000000..a4b6f05d4
--- /dev/null
+++ b/modules/nf-core/rseqc/tin/tests/main.nf.test
@@ -0,0 +1,54 @@
+nextflow_process {
+
+    name "Test Process RSEQC_TIN"
+    script "../main.nf"
+    process "RSEQC_TIN"
+
+    test("sarscov2 paired-end [bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/rseqc/tin/tests/main.nf.test.snap b/modules/nf-core/rseqc/tin/tests/main.nf.test.snap
new file mode 100644
index 000000000..caab3a091
--- /dev/null
+++ b/modules/nf-core/rseqc/tin/tests/main.nf.test.snap
@@ -0,0 +1,108 @@
+{
+    "sarscov2 paired-end [bam]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.summary.txt:md5,9d98447e178b89a89f6f5aba7a772fe6"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.tin.xls:md5,abdbb6d51a5cd7038cd862ce241ecef1"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,79670dedaa11a978951c16ead7f49c24"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.summary.txt:md5,9d98447e178b89a89f6f5aba7a772fe6"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,79670dedaa11a978951c16ead7f49c24"
+                ],
+                "xls": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.tin.xls:md5,abdbb6d51a5cd7038cd862ce241ecef1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-26T14:32:42.823857"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.tin.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,79670dedaa11a978951c16ead7f49c24"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,79670dedaa11a978951c16ead7f49c24"
+                ],
+                "xls": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.tin.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T09:55:57.905927"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml
new file mode 100644
index 000000000..a6607d964
--- /dev/null
+++ b/modules/nf-core/salmon/index/environment.yml
@@ -0,0 +1,7 @@
+name: salmon_index
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::salmon=1.10.1
diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf
index 118ee6704..e755d9a34 100644
--- a/modules/nf-core/salmon/index/main.nf
+++ b/modules/nf-core/salmon/index/main.nf
@@ -2,7 +2,7 @@ process SALMON_INDEX {
     tag "$transcript_fasta"
     label "process_medium"
 
-    conda "bioconda::salmon=1.10.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' :
         'biocontainers/salmon:1.10.1--h7e5ed60_0' }"
@@ -44,4 +44,29 @@ process SALMON_INDEX {
         salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir salmon
+    touch salmon/complete_ref_lens.bin
+    touch salmon/ctable.bin
+    touch salmon/ctg_offsets.bin
+    touch salmon/duplicate_clusters.tsv
+    touch salmon/info.json
+    touch salmon/mphf.bin
+    touch salmon/pos.bin
+    touch salmon/pre_indexing.log
+    touch salmon/rank.bin
+    touch salmon/refAccumLengths.bin
+    touch salmon/ref_indexing.log
+    touch salmon/reflengths.bin
+    touch salmon/refseq.bin
+    touch salmon/seq.bin
+    touch salmon/versionInfo.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/salmon/index/meta.yml b/modules/nf-core/salmon/index/meta.yml
index 53c64152f..fd94dd274 100644
--- a/modules/nf-core/salmon/index/meta.yml
+++ b/modules/nf-core/salmon/index/meta.yml
@@ -20,7 +20,6 @@ input:
   - transcriptome_fasta:
       type: file
       description: Fasta file of the reference transcriptome
-
 output:
   - index:
       type: directory
@@ -30,7 +29,9 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@kevinmenden"
   - "@drpatelh"
+maintainers:
+  - "@kevinmenden"
+  - "@drpatelh"
diff --git a/modules/nf-core/salmon/index/tests/main.nf.test b/modules/nf-core/salmon/index/tests/main.nf.test
new file mode 100644
index 000000000..0caf30d3e
--- /dev/null
+++ b/modules/nf-core/salmon/index/tests/main.nf.test
@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process SALMON_INDEX"
+    script "../main.nf"
+    process "SALMON_INDEX"
+
+    test("sarscov2") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.index.get(0)).exists() },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+     test("sarscov2 stub") {
+        options "-stub"
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.index.get(0)).exists() },
+                { assert snapshot(process.out.versions).match("versions stub") }
+            )
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/salmon/index/tests/main.nf.test.snap b/modules/nf-core/salmon/index/tests/main.nf.test.snap
new file mode 100644
index 000000000..703e455c5
--- /dev/null
+++ b/modules/nf-core/salmon/index/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2023-11-22T14:26:33.32036"
+    },
+    "versions stub": {
+        "content": [
+            [
+                "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-23T09:47:58.828124"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml
new file mode 100644
index 000000000..862667241
--- /dev/null
+++ b/modules/nf-core/salmon/quant/environment.yml
@@ -0,0 +1,7 @@
+name: salmon_quant
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::salmon=1.10.1
diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf
index f11b6c2e2..6c528b240 100644
--- a/modules/nf-core/salmon/quant/main.nf
+++ b/modules/nf-core/salmon/quant/main.nf
@@ -2,7 +2,7 @@ process SALMON_QUANT {
     tag "$meta.id"
     label "process_medium"
 
-    conda "bioconda::salmon=1.10.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' :
         'biocontainers/salmon:1.10.1--h7e5ed60_0' }"
@@ -16,9 +16,10 @@ process SALMON_QUANT {
     val   lib_type
 
     output:
-    tuple val(meta), path("${prefix}") , emit: results
-    tuple val(meta), path("*info.json"), emit: json_info, optional: true
-    path  "versions.yml"               , emit: versions
+    tuple val(meta), path("${prefix}")              , emit: results
+    tuple val(meta), path("*info.json")             , emit: json_info, optional: true
+    tuple val(meta), path("*lib_format_counts.json"), emit: lib_format_counts, optional: true
+    path  "versions.yml"                            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -70,6 +71,22 @@ process SALMON_QUANT {
     if [ -f $prefix/aux_info/meta_info.json ]; then
         cp $prefix/aux_info/meta_info.json "${prefix}_meta_info.json"
     fi
+    if [ -f $prefix/lib_format_counts.json ]; then
+        cp $prefix/lib_format_counts.json "${prefix}_lib_format_counts.json"
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    touch ${prefix}_meta_info.json
+    touch ${prefix}_lib_format_counts.json
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/salmon/quant/meta.yml b/modules/nf-core/salmon/quant/meta.yml
index e809ade2b..a2faf589a 100644
--- a/modules/nf-core/salmon/quant/meta.yml
+++ b/modules/nf-core/salmon/quant/meta.yml
@@ -31,7 +31,7 @@ input:
   - gtf:
       type: file
       description: GTF of the reference transcriptome
-  - transcriptome_fasta:
+  - transcript_fasta:
       type: file
       description: Fasta file of the reference transcriptome
   - alignment_mode:
@@ -41,7 +41,6 @@ input:
       type: string
       description: |
         Override library type inferred based on strandedness defined in meta object
-
 output:
   - results:
       type: directory
@@ -55,7 +54,9 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@kevinmenden"
   - "@drpatelh"
+maintainers:
+  - "@kevinmenden"
+  - "@drpatelh"
diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test b/modules/nf-core/salmon/quant/tests/main.nf.test
new file mode 100644
index 000000000..24d8dd700
--- /dev/null
+++ b/modules/nf-core/salmon/quant/tests/main.nf.test
@@ -0,0 +1,315 @@
+nextflow_process {
+
+    name "Test Process SALMON_QUANT"
+    script "../main.nf"
+    process "SALMON_QUANT"
+    config "./nextflow.config"
+
+    setup {
+        run("SALMON_INDEX") {
+            script "../../../salmon/index/main.nf"
+            process {
+                """
+                input[0] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - single_end") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.lib_format_counts
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - single_end stub") {
+        options "-stub"
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.lib_format_counts
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - single_end lib type A") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = 'A'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.lib_format_counts
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - single_end lib type A stub") {
+        options "-stub"
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = 'A'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.lib_format_counts
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - pair_end") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.lib_format_counts
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - pair_end stub") {
+        options "-stub"
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: true ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.lib_format_counts
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - pair_end multiple") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test2_2.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.lib_format_counts
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - pair_end multiple stub") {
+        options "-stub"
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test2_2.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = SALMON_INDEX.out.index
+                input[2] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)])
+                input[3] = Channel.of([file(params.modules_testdata_base_path + "genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)])
+                input[4] = false
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json_info.get(0).get(1)).exists() },
+                { assert path(process.out.results.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.lib_format_counts
+                ).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test.snap b/modules/nf-core/salmon/quant/tests/main.nf.test.snap
new file mode 100644
index 000000000..547ce2de1
--- /dev/null
+++ b/modules/nf-core/salmon/quant/tests/main.nf.test.snap
@@ -0,0 +1,170 @@
+{
+    "sarscov2 - single_end": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_lib_format_counts.json:md5,c7999dfccd32c090d94e5951522eecd4"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-14T09:51:22.424672"
+    },
+    "sarscov2 - single_end stub": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_lib_format_counts.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-14T09:51:32.292277"
+    },
+    "sarscov2 - single_end lib type A": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_lib_format_counts.json:md5,c7999dfccd32c090d94e5951522eecd4"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-14T09:51:42.656382"
+    },
+    "sarscov2 - pair_end multiple": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_lib_format_counts.json:md5,4a2ee0fac91a4a3471872808d8bd3ff8"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-14T09:52:33.03647"
+    },
+    "sarscov2 - pair_end multiple stub": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_lib_format_counts.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-14T09:52:43.388379"
+    },
+    "sarscov2 - single_end lib type A stub": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_lib_format_counts.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-14T09:51:52.612664"
+    },
+    "sarscov2 - pair_end": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_lib_format_counts.json:md5,e9516e73c9fb39145513b2a41a0af95f"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-14T09:52:05.577881"
+    },
+    "sarscov2 - pair_end stub": {
+        "content": [
+            [
+                "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_lib_format_counts.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-14T09:52:15.286461"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/salmon/quant/tests/nextflow.config b/modules/nf-core/salmon/quant/tests/nextflow.config
new file mode 100644
index 000000000..37c082129
--- /dev/null
+++ b/modules/nf-core/salmon/quant/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SALMON_QUANT {
+        ext.args = '--minAssignedFrags 1'
+    }
+
+}
diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml
new file mode 100644
index 000000000..68b81558e
--- /dev/null
+++ b/modules/nf-core/samtools/flagstat/environment.yml
@@ -0,0 +1,8 @@
+name: samtools_flagstat
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
index b75707eca..754d84b73 100644
--- a/modules/nf-core/samtools/flagstat/main.nf
+++ b/modules/nf-core/samtools/flagstat/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::samtools=1.17"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml
index 954225dfc..97991358e 100644
--- a/modules/nf-core/samtools/flagstat/meta.yml
+++ b/modules/nf-core/samtools/flagstat/meta.yml
@@ -47,3 +47,5 @@ output:
       pattern: "versions.yml"
 authors:
   - "@drpatelh"
+maintainers:
+  - "@drpatelh"
diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test
new file mode 100644
index 000000000..b899f1fc7
--- /dev/null
+++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test
@@ -0,0 +1,52 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_FLAGSTAT"
+    script "../main.nf"
+    process "SAMTOOLS_FLAGSTAT"
+
+    test("BAM") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("BAM - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
new file mode 100644
index 000000000..23989c612
--- /dev/null
+++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "BAM - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2"
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:17:28.002887"
+    },
+    "BAM": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2"
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:17:13.330971"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml
new file mode 100644
index 000000000..eb6c88099
--- /dev/null
+++ b/modules/nf-core/samtools/idxstats/environment.yml
@@ -0,0 +1,8 @@
+name: samtools_idxstats
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
index 83c7c34b9..2ea2a5ccd 100644
--- a/modules/nf-core/samtools/idxstats/main.nf
+++ b/modules/nf-core/samtools/idxstats/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::samtools=1.17"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml
index dda87e1ee..344e92a3f 100644
--- a/modules/nf-core/samtools/idxstats/meta.yml
+++ b/modules/nf-core/samtools/idxstats/meta.yml
@@ -48,3 +48,5 @@ output:
       pattern: "versions.yml"
 authors:
   - "@drpatelh"
+maintainers:
+  - "@drpatelh"
diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test
new file mode 100644
index 000000000..bf4c31047
--- /dev/null
+++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test
@@ -0,0 +1,49 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_IDXSTATS"
+    script "../main.nf"
+    process "SAMTOOLS_IDXSTATS"
+
+    test("bam") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("bam - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }}
diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap
new file mode 100644
index 000000000..a5ac8104e
--- /dev/null
+++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351"
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:17:56.180093"
+    },
+    "bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351"
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:17:41.408704"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml
new file mode 100644
index 000000000..260d516be
--- /dev/null
+++ b/modules/nf-core/samtools/index/environment.yml
@@ -0,0 +1,8 @@
+name: samtools_index
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index 0b20aa4bb..e002585b9 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::samtools=1.17"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input)
@@ -35,10 +35,11 @@ process SAMTOOLS_INDEX {
     """
 
     stub:
+    def args = task.ext.args ?: ''
+    def extension = file(input).getExtension() == 'cram' ?
+                    "crai" : args.contains("-c") ?  "csi" : "bai"
     """
-    touch ${input}.bai
-    touch ${input}.crai
-    touch ${input}.csi
+    touch ${input}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
index 8bd2fa6fb..01a4ee03e 100644
--- a/modules/nf-core/samtools/index/meta.yml
+++ b/modules/nf-core/samtools/index/meta.yml
@@ -51,3 +51,7 @@ authors:
   - "@drpatelh"
   - "@ewels"
   - "@maxulysse"
+maintainers:
+  - "@drpatelh"
+  - "@ewels"
+  - "@maxulysse"
diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config
new file mode 100644
index 000000000..0ed260efa
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SAMTOOLS_INDEX {
+        ext.args = '-c'
+    }
+
+}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test
new file mode 100644
index 000000000..b59a25b38
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/main.nf.test
@@ -0,0 +1,136 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_INDEX"
+    script "../main.nf"
+    process "SAMTOOLS_INDEX"
+
+    test("bai") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("crai") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("csi") {
+        config "./csi.nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.csi[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("bai - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("crai - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("csi - stub") {
+        options "-stub"
+        config "./csi.nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap
new file mode 100644
index 000000000..799d199ce
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap
@@ -0,0 +1,250 @@
+{
+    "csi - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    
+                ],
+                "crai": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:53.9057"
+    },
+    "crai - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:45.931558"
+    },
+    "bai - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:34.807525"
+    },
+    "csi": {
+        "content": [
+            "test.paired_end.sorted.bam.csi",
+            [
+                "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:52:55.688799"
+    },
+    "crai": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:17.609533"
+    },
+    "bai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:04.16585"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml
new file mode 100644
index 000000000..36a12eab0
--- /dev/null
+++ b/modules/nf-core/samtools/sort/environment.yml
@@ -0,0 +1,8 @@
+name: samtools_sort
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 2b7753fd8..8e019099c 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -2,17 +2,20 @@ process SAMTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::samtools=1.17"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta) , path(bam)
+    tuple val(meta2), path(fasta)
 
     output:
-    tuple val(meta), path("*.bam"), emit: bam
-    tuple val(meta), path("*.csi"), emit: csi, optional: true
+    tuple val(meta), path("*.bam"),     emit: bam,  optional: true
+    tuple val(meta), path("*.cram"),    emit: cram, optional: true
+    tuple val(meta), path("*.crai"),    emit: crai, optional: true
+    tuple val(meta), path("*.csi"),     emit: csi,  optional: true
     path  "versions.yml"          , emit: versions
 
     when:
@@ -21,14 +24,24 @@ process SAMTOOLS_SORT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--output-fmt sam") ? "sam" :
+                    args.contains("--output-fmt cram") ? "cram" :
+                    "bam"
+    def reference = fasta ? "--reference ${fasta}" : ""
     if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+
     """
+    samtools cat \\
+        --threads $task.cpus \\
+        ${bam} \\
+    | \\
     samtools sort \\
         $args \\
-        -@ $task.cpus \\
-        -o ${prefix}.bam \\
-        -T $prefix \\
-        $bam
+        -T ${prefix} \\
+        --threads $task.cpus \\
+        ${reference} \\
+        -o ${prefix}.${extension} \\
+        -
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -37,9 +50,20 @@ process SAMTOOLS_SORT {
     """
 
     stub:
+    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--output-fmt sam") ? "sam" :
+                    args.contains("--output-fmt cram") ? "cram" :
+                    "bam"
     """
-    touch ${prefix}.bam
+    touch ${prefix}.${extension}
+    if [ "${extension}" == "bam" ];
+    then
+        touch ${prefix}.${extension}.csi
+    elif [ "${extension}" == "cram" ];
+    then
+        touch ${prefix}.${extension}.crai
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 073284316..341a7d0eb 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -23,8 +23,18 @@ input:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: BAM/CRAM/SAM file
+      description: BAM/CRAM/SAM file(s)
       pattern: "*.{bam,cram,sam}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
+  - fasta:
+      type: file
+      description: Reference genome FASTA file
+      pattern: "*.{fa,fasta,fna}"
+      optional: true
 output:
   - meta:
       type: map
@@ -33,16 +43,29 @@ output:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
-  - versions:
+      description: Sorted BAM file
+      pattern: "*.{bam}"
+  - cram:
       type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      description: Sorted CRAM file
+      pattern: "*.{cram}"
+  - crai:
+      type: file
+      description: CRAM index file (optional)
+      pattern: "*.crai"
   - csi:
       type: file
       description: BAM index file (optional)
       pattern: "*.csi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@ewels"
+  - "@matthdsm"
+maintainers:
+  - "@drpatelh"
+  - "@ewels"
+  - "@matthdsm"
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test
new file mode 100644
index 000000000..41c2fca7f
--- /dev/null
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test
@@ -0,0 +1,124 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_SORT"
+    script "../main.nf"
+    process "SAMTOOLS_SORT"
+
+    test("bam") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                        process.out.bam,
+                        process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                        process.out.versions
+                ).match()}
+            )
+        }
+    }
+
+    test("cram") {
+
+        config "./nextflow_cram.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                    process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                    process.out.versions
+                ).match()}
+            )
+        }
+    }
+
+    test("bam - stub") {
+
+        options "-stub"
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("cram - stub") {
+
+        options "-stub"
+        config "./nextflow_cram.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
new file mode 100644
index 000000000..da38d5d15
--- /dev/null
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
@@ -0,0 +1,192 @@
+{
+    "cram": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.cram"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.cram.crai"
+                ]
+            ],
+            [
+                "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:19:37.196205"
+    },
+    "bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T15:54:46.580756"
+    },
+    "cram - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                ],
+                "bam": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T15:57:30.505698"
+    },
+    "bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam.csi"
+                ]
+            ],
+            [
+                "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T15:54:25.872954"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config
new file mode 100644
index 000000000..f642771f5
--- /dev/null
+++ b/modules/nf-core/samtools/sort/tests/nextflow.config
@@ -0,0 +1,8 @@
+process {
+
+    withName: SAMTOOLS_SORT {
+        ext.prefix  = { "${meta.id}.sorted" }
+        ext.args    = "--write-index"
+    }
+
+}
diff --git a/modules/nf-core/samtools/sort/tests/nextflow_cram.config b/modules/nf-core/samtools/sort/tests/nextflow_cram.config
new file mode 100644
index 000000000..3a8c0188b
--- /dev/null
+++ b/modules/nf-core/samtools/sort/tests/nextflow_cram.config
@@ -0,0 +1,8 @@
+process {
+
+    withName: SAMTOOLS_SORT {
+        ext.prefix  = { "${meta.id}.sorted" }
+        ext.args    = "--write-index --output-fmt cram"
+    }
+
+}
diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml
new file mode 100644
index 000000000..1cc83bd95
--- /dev/null
+++ b/modules/nf-core/samtools/stats/environment.yml
@@ -0,0 +1,8 @@
+name: samtools_stats
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
index 4a2607ded..982bc28e7 100644
--- a/modules/nf-core/samtools/stats/main.nf
+++ b/modules/nf-core/samtools/stats/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_STATS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::samtools=1.17"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml
index 90e6345f5..735ff8122 100644
--- a/modules/nf-core/samtools/stats/meta.yml
+++ b/modules/nf-core/samtools/stats/meta.yml
@@ -57,3 +57,7 @@ authors:
   - "@drpatelh"
   - "@FriederikeHanssen"
   - "@ramprasadn"
+maintainers:
+  - "@drpatelh"
+  - "@FriederikeHanssen"
+  - "@ramprasadn"
diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test
new file mode 100644
index 000000000..6416ae127
--- /dev/null
+++ b/modules/nf-core/samtools/stats/tests/main.nf.test
@@ -0,0 +1,108 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_STATS"
+    script "../main.nf"
+    process "SAMTOOLS_STATS"
+
+    test("bam") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                {assert process.success},
+                {assert snapshot(process.out).match()}
+            )
+        }
+    }
+
+    test("cram") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                {assert process.success},
+                {assert snapshot(process.out).match()}
+            )
+        }
+    }
+
+    test("bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                {assert process.success},
+                {assert snapshot(process.out).match()}
+            )
+        }
+    }
+
+    test("cram - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                {assert process.success},
+                {assert snapshot(process.out).match()}
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap
new file mode 100644
index 000000000..3828f3788
--- /dev/null
+++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap
@@ -0,0 +1,142 @@
+{
+    "cram": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,c9d39b38c22de2057fc2f89949090975"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,c9d39b38c22de2057fc2f89949090975"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:20:24.885816"
+    },
+    "bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:20:39.310713"
+    },
+    "cram - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:21:04.771199"
+    },
+    "bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:19:06.645466"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml
new file mode 100644
index 000000000..f40f9958d
--- /dev/null
+++ b/modules/nf-core/sortmerna/environment.yml
@@ -0,0 +1,7 @@
+name: sortmerna
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::sortmerna=4.3.6
diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf
index 7afae5a68..7c17e500c 100644
--- a/modules/nf-core/sortmerna/main.nf
+++ b/modules/nf-core/sortmerna/main.nf
@@ -1,70 +1,110 @@
 process SORTMERNA {
     tag "$meta.id"
-    label "process_high"
+    label 'process_high'
 
-    conda "bioconda::sortmerna=4.3.4"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sortmerna:4.3.4--h9ee0642_0' :
-        'biocontainers/sortmerna:4.3.4--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' :
+        'biocontainers/sortmerna:4.3.6--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(reads)
-    path  fastas
+    tuple val(meta2), path(fastas)
+    tuple val(meta3), path(index)
 
     output:
-    tuple val(meta), path("*non_rRNA.fastq.gz"), emit: reads
-    tuple val(meta), path("*.log")     , emit: log
-    path  "versions.yml"               , emit: versions
+    tuple val(meta), path("*non_rRNA.fastq.gz"), emit: reads, optional: true
+    tuple val(meta), path("*.log")             , emit: log, optional: true
+    tuple val(meta2), path("idx")              , emit: index, optional: true
+    path  "versions.yml"                       , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        """
-        sortmerna \\
-            ${'--ref '+fastas.join(' --ref ')} \\
-            --reads $reads \\
-            --threads $task.cpus \\
-            --workdir . \\
-            --aligned rRNA_reads \\
-            --fastx \\
-            --other non_rRNA_reads \\
-            $args
+    def args          = task.ext.args  ?: ''
+    def prefix        = task.ext.prefix ?: "${meta.id}"
 
-        mv non_rRNA_reads.f*q.gz ${prefix}.non_rRNA.fastq.gz
-        mv rRNA_reads.log ${prefix}.sortmerna.log
+    def index_only    = args.contains('--index 1')? true : false
+    def skip_index    = args.contains('--index 0')? true : false
+    def paired_end    = reads instanceof List
+    def paired_cmd    = ''
+    def reads_args    = ''
+    def out2_cmd      = ''
+    def mv_cmd        = ''
+    def reads_input   = ''
+    def refs_input    = ''
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
-        END_VERSIONS
-        """
-    } else {
-        """
-        sortmerna \\
-            ${'--ref '+fastas.join(' --ref ')} \\
-            --reads ${reads[0]} \\
-            --reads ${reads[1]} \\
-            --threads $task.cpus \\
-            --workdir . \\
-            --aligned rRNA_reads \\
-            --fastx \\
-            --other non_rRNA_reads \\
-            --paired_in \\
-            --out2 \\
-            $args
+    if (! index_only){
+        reads_args = '--aligned rRNA_reads --fastx --other non_rRNA_reads'
+        reads_input = paired_end ? reads.collect{"--reads $it"}.join(' ') : "--reads $reads"
+        def n_fastq = paired_end ? reads.size() : 1
+        if ( n_fastq == 1 ) {
+            mv_cmd = """
+            mv non_rRNA_reads.f*q.gz ${prefix}.non_rRNA.fastq.gz
+            mv rRNA_reads.log ${prefix}.sortmerna.log
+            """
+        } else {
+            mv_cmd = """
+            mv non_rRNA_reads_fwd.f*q.gz ${prefix}_1.non_rRNA.fastq.gz
+            mv non_rRNA_reads_rev.f*q.gz ${prefix}_2.non_rRNA.fastq.gz
+            mv rRNA_reads.log ${prefix}.sortmerna.log
+            """
+            paired_cmd = "--paired_in"
+            out2_cmd   = "--out2"
+        }
+    }
+    """
+    sortmerna \\
+        ${'--ref '+fastas.join(' --ref ')} \\
+        $refs_input \\
+        $reads_input \\
+        --threads $task.cpus \\
+        --workdir . \\
+        $reads_args \\
+        $paired_cmd \\
+        $out2_cmd \\
+        $args
+
+    $mv_cmd
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
+    END_VERSIONS
+    """
 
-        mv non_rRNA_reads_fwd.f*q.gz ${prefix}_1.non_rRNA.fastq.gz
-        mv non_rRNA_reads_rev.f*q.gz ${prefix}_2.non_rRNA.fastq.gz
-        mv rRNA_reads.log ${prefix}.sortmerna.log
+    stub:
+    def args          = task.ext.args  ?: ''
+    def prefix        = task.ext.prefix ?: "${meta.id}"
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
-        END_VERSIONS
-        """
+    def index_only    = args.contains('--index 1')? true : false
+    def paired_end    = reads instanceof List
+    def paired_cmd    = ''
+    def out2_cmd      = ''
+    def mv_cmd        = ''
+    def reads_input   = ''
+
+    if (! index_only){
+        reads_input = paired_end ? reads.collect{"--reads $it"}.join(' ') : "--reads $reads"
+        def n_fastq = paired_end ? reads.size() : 1
+        if ( n_fastq == 1 ) {
+            mv_cmd = "touch ${prefix}.non_rRNA.fastq.gz"
+        } else {
+            mv_cmd = """
+            touch ${prefix}_1.non_rRNA.fastq.gz
+            touch ${prefix}_2.non_rRNA.fastq.gz
+            """
+        }
     }
+    """
+    $mv_cmd
+    mkdir -p idx
+    touch ${prefix}.sortmerna.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/sortmerna/meta.yml b/modules/nf-core/sortmerna/meta.yml
index 516d11606..c0a2a581f 100644
--- a/modules/nf-core/sortmerna/meta.yml
+++ b/modules/nf-core/sortmerna/meta.yml
@@ -23,16 +23,31 @@ input:
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively.
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - fastas:
       type: file
       description: |
         Path to reference file(s)
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing index information
+        e.g. [ id:'test' ]
+  - index:
+      type: directory
+      description: |
+        Path to index directory of a previous sortmerna run
 output:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test', single_end:false ], or reference information from an
+        indexing-only run
   - reads:
       type: file
       description: The filtered fastq reads
@@ -41,6 +56,15 @@ output:
       type: file
       description: SortMeRNA log file
       pattern: "*sortmerna.log"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
+  - index:
+      type: directory
+      description: |
+        Path to index directory generated by sortmern
   - versions:
       type: file
       description: File containing software versions
@@ -48,3 +72,6 @@ output:
 authors:
   - "@drpatelh"
   - "@mashehu"
+maintainers:
+  - "@drpatelh"
+  - "@mashehu"
diff --git a/modules/nf-core/sortmerna/nextflow.config b/modules/nf-core/sortmerna/nextflow.config
new file mode 100644
index 000000000..953da5a39
--- /dev/null
+++ b/modules/nf-core/sortmerna/nextflow.config
@@ -0,0 +1,20 @@
+if (params.remove_ribo_rna) {
+    process {
+        withName: 'SORTMERNA' {
+            ext.args   = '--num_alignments 1 -v --index 0'
+            publishDir = [
+                [
+                    path: { "${params.outdir}/sortmerna" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.log"
+                ],
+                [
+                    path: { params.save_non_ribo_reads ? "${params.outdir}/sortmerna" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz",
+                    saveAs: { params.save_non_ribo_reads ? it : null }
+                ]
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sortmerna/tests/indexing_only.config b/modules/nf-core/sortmerna/tests/indexing_only.config
new file mode 100644
index 000000000..3e74a3229
--- /dev/null
+++ b/modules/nf-core/sortmerna/tests/indexing_only.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'SORTMERNA' {
+        ext.args  = '--index 1'
+    }
+}
diff --git a/modules/nf-core/sortmerna/tests/main.nf.test b/modules/nf-core/sortmerna/tests/main.nf.test
new file mode 100644
index 000000000..1954bdfb0
--- /dev/null
+++ b/modules/nf-core/sortmerna/tests/main.nf.test
@@ -0,0 +1,324 @@
+nextflow_process {
+
+    name "Test Process SORTMERNA"
+    script "../main.nf"
+    process "SORTMERNA"
+
+    test("sarscov2 indexing only") {
+
+        config './indexing_only.config'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([[],[]])
+                input[1] = [ [id:'test2'], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                ]
+                input[2] = Channel.of([[],[]])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert ! process.out.reads },
+                { assert snapshot(process.out.index).match("index_index_only") },
+                { assert snapshot(process.out.versions).match("versions_index_only") }
+            )
+        }
+
+    }
+    
+    test("sarscov2 indexing only stub") {
+ 
+        options '-stub'
+        config './indexing_only.config'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([[],[]])
+                input[1] = [ [id:'test2'], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                ]
+                input[2] = Channel.of([[],[]])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert ! process.out.reads },
+                { assert snapshot(process.out.index).match("index_only_stub") },
+                { assert snapshot(process.out.versions).match("versions_index_only_stub") }
+            )
+        }
+
+    }
+
+    test("sarscov2 single_end") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ]
+                input[1] = [ [id:'test2'], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                ]
+                input[2] = Channel.of([[],[]])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.reads },
+                { assert file(process.out.log[0][1]).text.contains("Total reads passing E-value threshold = 100 (100.00)") },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("sarscov2 single_end_match")
+                },
+                { assert snapshot(process.out.index).match("index_single_end") },
+                { assert snapshot(process.out.versions).match("versions_single_end") }
+            )
+        }
+
+    }
+
+    test("sarscov2 single_end stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ]
+                input[1] = [ [id:'test2'], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                ]
+                input[2] = Channel.of([[],[]])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("sarscov2 single_end-for_stub_match")
+                },
+                { assert snapshot(process.out.index).match("index_single_end_stub") },
+                { assert snapshot(process.out.versions).match("versions_single_end_stub") }
+            )
+        }
+
+    }
+
+    test("sarscov2 paired_end") {
+
+        when {
+            process {
+                """
+                input[0] = [ 
+                    [ id:'test' ], // meta map
+                    [ 
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ]
+                input[1] = [ [id:'test2'], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                ]
+                input[2] = Channel.of([[],[]])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.reads },
+                { assert file(process.out.log[0][1]).text.contains("Total reads passing E-value threshold = 200 (100.00)") },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { it[1].collect { item -> file(item).getName() } } +
+                            process.out.log.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("sarscov2 paired_end_match")
+                },
+                { assert snapshot(process.out.index).match("index_paired_end") },
+                { assert snapshot(process.out.versions).match("versions_paired_end") }
+            )
+        }
+
+    }
+
+    test("sarscov2 paired_end stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    [ 
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ]
+                input[1] = [ [id:'test2'], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                ]
+                input[2] = Channel.of([[],[]])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { it[1].collect { item -> file(item).getName() } } +
+                            process.out.log.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("sarscov2 paired_end-for_stub_match")
+                },
+                { assert snapshot(process.out.index).match("index_paired_end_stub") },
+                { assert snapshot(process.out.versions).match("versions_paired_end_stub") }
+            )
+        }
+
+    }
+
+    test("sarscov2 single_end premade_index") {
+
+        config './premade_index.config'
+    
+        setup {
+
+            run("SORTMERNA", alias: "SORTMERNA_INDEX") {
+                script "../main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([[],[]])
+                    input[1] = [ [id:'test2'], // meta map
+                        [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                    ]
+                    input[2] = Channel.of([[],[]])
+                    """
+                }
+            }
+        }
+        
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ]
+                input[1] = [ [id:'test2'], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                ]
+                input[2] = SORTMERNA_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.reads },
+                { assert file(process.out.log[0][1]).text.contains("Total reads passing E-value threshold = 100 (100.00)") },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("sarscov2 single_end_premade_index_match")
+                },
+                { assert snapshot(process.out.index).match("index_single_end_premade_index") },
+                { assert snapshot(process.out.versions).match("versions_single_end_premade_index") }
+            )
+        }
+    }
+
+    test("sarscov2 single_end premade_index stub") {
+
+        config './premade_index.config'
+        options '-stub'
+    
+        setup {
+
+            run("SORTMERNA", alias: "SORTMERNA_INDEX") {
+                script "../main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([[],[]])
+                    input[1] = [ [id:'test2'], // meta map
+                        [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                    ]
+                    input[2] = Channel.of([[],[]])
+                    """
+                }
+            }
+        }
+        
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ]
+                input[1] = [ [id:'test2'], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
+                ]
+                input[2] = SORTMERNA_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.reads },
+                {
+                    assert snapshot(
+                        (
+                            [process.out.reads[0][0].toString()] + // meta
+                            process.out.reads.collect { file(it[1]).getName() } +
+                            process.out.log.collect { file(it[1]).getName() }
+                        ).sort()
+                    ).match("sarscov2 single_end_premade_index_match_stub")
+                },
+                { assert snapshot(process.out.index).match("index_single_end_premade_index_stub") },
+                { assert snapshot(process.out.versions).match("versions_single_end_premade_index_stub") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/sortmerna/tests/main.nf.test.snap b/modules/nf-core/sortmerna/tests/main.nf.test.snap
new file mode 100644
index 000000000..86e84733b
--- /dev/null
+++ b/modules/nf-core/sortmerna/tests/main.nf.test.snap
@@ -0,0 +1,352 @@
+{
+    "versions_paired_end_stub": {
+        "content": [
+            [
+                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-07T12:27:11.223149"
+    },
+    "index_paired_end_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test2"
+                    },
+                    [
+                        
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T14:24:25.384097178"
+    },
+    "versions_paired_end": {
+        "content": [
+            [
+                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-07T12:27:04.517155"
+    },
+    "versions_single_end_stub": {
+        "content": [
+            [
+                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T12:10:35.228450189"
+    },
+    "sarscov2 single_end_match": {
+        "content": [
+            [
+                "test.non_rRNA.fastq.gz",
+                "test.sortmerna.log",
+                "{id=test}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-07T12:28:23.20327"
+    },
+    "index_only_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test2"
+                    },
+                    [
+                        
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:00:47.128504164"
+    },
+    "index_single_end_premade_index": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test2"
+                    },
+                    [
+                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
+                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:01:53.832643452"
+    },
+    "versions_single_end_premade_index": {
+        "content": [
+            [
+                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:01:53.902154982"
+    },
+    "sarscov2 paired_end-for_stub_match": {
+        "content": [
+            [
+                "{id=test}",
+                [
+                    "test_1.non_rRNA.fastq.gz",
+                    "test_2.non_rRNA.fastq.gz"
+                ],
+                "test.sortmerna.log"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-07T12:28:56.063579"
+    },
+    "index_paired_end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test2"
+                    },
+                    [
+                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
+                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T14:24:14.272659781"
+    },
+    "sarscov2 single_end_premade_index_match_stub": {
+        "content": [
+            [
+                "test.non_rRNA.fastq.gz",
+                "test.sortmerna.log",
+                "{id=test}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:05:01.913287272"
+    },
+    "sarscov2 single_end-for_stub_match": {
+        "content": [
+            [
+                "test.non_rRNA.fastq.gz",
+                "test.sortmerna.log",
+                "{id=test}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-07T12:28:29.197913"
+    },
+    "sarscov2 paired_end_match": {
+        "content": [
+            [
+                "{id=test}",
+                [
+                    "test_1.non_rRNA.fastq.gz",
+                    "test_2.non_rRNA.fastq.gz"
+                ],
+                "test.sortmerna.log"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-07T12:28:49.914992"
+    },
+    "versions_single_end": {
+        "content": [
+            [
+                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T14:36:27.14244294"
+    },
+    "versions_index_only": {
+        "content": [
+            [
+                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:00:35.609161481"
+    },
+    "versions_single_end_premade_index_stub": {
+        "content": [
+            [
+                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:05:02.059858431"
+    },
+    "index_single_end_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test2"
+                    },
+                    [
+                        
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T14:23:58.068772508"
+    },
+    "versions_index_only_stub": {
+        "content": [
+            [
+                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:00:47.169402699"
+    },
+    "index_single_end_premade_index_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test2"
+                    },
+                    [
+                        
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:05:01.953316205"
+    },
+    "index_single_end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test2"
+                    },
+                    [
+                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
+                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T14:36:26.88061978"
+    },
+    "index_index_only": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test2"
+                    },
+                    [
+                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
+                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:00:35.34089252"
+    },
+    "sarscov2 single_end_premade_index_match": {
+        "content": [
+            [
+                "test.non_rRNA.fastq.gz",
+                "test.sortmerna.log",
+                "{id=test}"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-26T15:01:53.797737296"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sortmerna/tests/premade_index.config b/modules/nf-core/sortmerna/tests/premade_index.config
new file mode 100644
index 000000000..ab86d2e62
--- /dev/null
+++ b/modules/nf-core/sortmerna/tests/premade_index.config
@@ -0,0 +1,8 @@
+process {
+    withName: 'SORTMERNA_INDEX' {
+        ext.args  = '--index 1'
+    }
+    withName: 'SORTMERNA' {
+        ext.args  = '--index 0'
+    }
+}
diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml
new file mode 100644
index 000000000..8bd58cff5
--- /dev/null
+++ b/modules/nf-core/star/align/environment.yml
@@ -0,0 +1,10 @@
+name: star_align
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::star=2.7.10a
+  - bioconda::samtools=1.18
+  - bioconda::htslib=1.18
+  - conda-forge::gawk=5.1.0
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
index d0e203848..ae67e0040 100644
--- a/modules/nf-core/star/align/main.nf
+++ b/modules/nf-core/star/align/main.nf
@@ -2,10 +2,10 @@ process STAR_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' :
-        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' :
+        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
@@ -81,6 +81,8 @@ process STAR_ALIGN {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    echo "" | gzip > ${prefix}.unmapped_1.fastq.gz
+    echo "" | gzip > ${prefix}.unmapped_2.fastq.gz
     touch ${prefix}Xd.out.bam
     touch ${prefix}.Log.final.out
     touch ${prefix}.Log.out
@@ -89,8 +91,6 @@ process STAR_ALIGN {
     touch ${prefix}.toTranscriptome.out.bam
     touch ${prefix}.Aligned.unsort.out.bam
     touch ${prefix}.Aligned.sortedByCoord.out.bam
-    touch ${prefix}.unmapped_1.fastq.gz
-    touch ${prefix}.unmapped_2.fastq.gz
     touch ${prefix}.tab
     touch ${prefix}.SJ.out.tab
     touch ${prefix}.ReadsPerGene.out.tab
diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml
index 3d8fed0cc..e80dbb7dd 100644
--- a/modules/nf-core/star/align/meta.yml
+++ b/modules/nf-core/star/align/meta.yml
@@ -52,7 +52,6 @@ input:
   - seq_center:
       type: string
       description: Sequencing center
-
 output:
   - bam:
       type: file
@@ -106,8 +105,11 @@ output:
       type: file
       description: STAR output bedGraph format file(s) (optional)
       pattern: "*.bg"
-
 authors:
   - "@kevinmenden"
   - "@drpatelh"
   - "@praveenraj2018"
+maintainers:
+  - "@kevinmenden"
+  - "@drpatelh"
+  - "@praveenraj2018"
diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test
new file mode 100644
index 000000000..69f655ef4
--- /dev/null
+++ b/modules/nf-core/star/align/tests/main.nf.test
@@ -0,0 +1,604 @@
+nextflow_process {
+
+    name "Test Process STAR_ALIGN"
+    script "../main.nf"
+    process "STAR_ALIGN"
+
+    test("homo_sapiens - single_end") {
+        config "./nextflow.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end") {
+        config "./nextflow.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - arriba") {
+        config "./nextflow.arriba.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - starfusion") {
+        config "./nextflow.starfusion.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - multiple") {
+        config "./nextflow.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log_final[0][1]).name,
+                    file(process.out.log_out[0][1]).name,
+                    file(process.out.log_progress[0][1]).name,
+                    process.out.bam,
+                    process.out.bam_sorted,
+                    process.out.bam_transcript,
+                    process.out.bam_unsorted,
+                    process.out.bedgraph,
+                    process.out.fastq,
+                    process.out.junction,
+                    process.out.read_per_gene_tab,
+                    process.out.sam,
+                    process.out.spl_junc_tab,
+                    process.out.tab,
+                    process.out.wig,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - single_end - stub") {
+        options "-stub"
+        config "./nextflow.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - stub") {
+        options "-stub"
+        config "./nextflow.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - arriba - stub") {
+        options "-stub"
+        config "./nextflow.arriba.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - starfusion - stub") {
+        options "-stub"
+        config "./nextflow.starfusion.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - paired_end - multiple - stub") {
+        options "-stub"
+        config "./nextflow.config"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = false
+                input[4] = 'illumina'
+                input[5] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap
new file mode 100644
index 000000000..c814eb56c
--- /dev/null
+++ b/modules/nf-core/star/align/tests/main.nf.test.snap
@@ -0,0 +1,1973 @@
+{
+    "homo_sapiens - single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "13": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "14": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "15": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam_sorted": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam_transcript": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_unsorted": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
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+                "13": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "14": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "15": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam_sorted": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "bam_transcript": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_unsorted": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "junction": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log_final": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log_out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log_progress": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "read_per_gene_tab": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "spl_junc_tab": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tab": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+                ],
+                "wig": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T15:16:40.64399"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/star/align/tests/nextflow.arriba.config b/modules/nf-core/star/align/tests/nextflow.arriba.config
new file mode 100644
index 000000000..2324b9e58
--- /dev/null
+++ b/modules/nf-core/star/align/tests/nextflow.arriba.config
@@ -0,0 +1,14 @@
+process {
+
+    withName: STAR_GENOMEGENERATE {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: STAR_ALIGN {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50'
+    }
+
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/modules/nf-core/star/align/tests/nextflow.config b/modules/nf-core/star/align/tests/nextflow.config
new file mode 100644
index 000000000..c4ac58088
--- /dev/null
+++ b/modules/nf-core/star/align/tests/nextflow.config
@@ -0,0 +1,14 @@
+process {
+
+    withName: STAR_GENOMEGENERATE {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: STAR_ALIGN {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded'
+    }
+
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/modules/nf-core/star/align/tests/nextflow.starfusion.config b/modules/nf-core/star/align/tests/nextflow.starfusion.config
new file mode 100644
index 000000000..467b64977
--- /dev/null
+++ b/modules/nf-core/star/align/tests/nextflow.starfusion.config
@@ -0,0 +1,14 @@
+process {
+
+    withName: STAR_GENOMEGENERATE {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: STAR_ALIGN {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outReadsUnmapped None --twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30'
+    }
+
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml
new file mode 100644
index 000000000..791f255e5
--- /dev/null
+++ b/modules/nf-core/star/genomegenerate/environment.yml
@@ -0,0 +1,10 @@
+name: star_genomegenerate
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::samtools=1.18
+  - bioconda::htslib=1.18
+  - bioconda::star=2.7.10a
+  - conda-forge::gawk=5.1.0
diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf
index 434240427..b8855715b 100644
--- a/modules/nf-core/star/genomegenerate/main.nf
+++ b/modules/nf-core/star/genomegenerate/main.nf
@@ -2,10 +2,10 @@ process STAR_GENOMEGENERATE {
     tag "$fasta"
     label 'process_high'
 
-    conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' :
-        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' :
+        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -19,9 +19,10 @@ process STAR_GENOMEGENERATE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def args_list = args.tokenize()
-    def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+    def args        = task.ext.args ?: ''
+    def args_list   = args.tokenize()
+    def memory      = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+    def include_gtf = gtf ? "--sjdbGTFfile $gtf" : ''
     if (args_list.contains('--genomeSAindexNbases')) {
         """
         mkdir star
@@ -29,7 +30,7 @@ process STAR_GENOMEGENERATE {
             --runMode genomeGenerate \\
             --genomeDir star/ \\
             --genomeFastaFiles $fasta \\
-            --sjdbGTFfile $gtf \\
+            $include_gtf \\
             --runThreadN $task.cpus \\
             $memory \\
             $args
@@ -51,7 +52,7 @@ process STAR_GENOMEGENERATE {
             --runMode genomeGenerate \\
             --genomeDir star/ \\
             --genomeFastaFiles $fasta \\
-            --sjdbGTFfile $gtf \\
+            $include_gtf \\
             --runThreadN $task.cpus \\
             --genomeSAindexNbases \$NUM_BASES \\
             $memory \\
@@ -67,30 +68,52 @@ process STAR_GENOMEGENERATE {
     }
 
     stub:
-    """
-    mkdir star
-    touch star/Genome
-    touch star/Log.out
-    touch star/SA
-    touch star/SAindex
-    touch star/chrLength.txt
-    touch star/chrName.txt
-    touch star/chrNameLength.txt
-    touch star/chrStart.txt
-    touch star/exonGeTrInfo.tab
-    touch star/exonInfo.tab
-    touch star/geneInfo.tab
-    touch star/genomeParameters.txt
-    touch star/sjdbInfo.txt
-    touch star/sjdbList.fromGTF.out.tab
-    touch star/sjdbList.out.tab
-    touch star/transcriptInfo.tab
+    if (gtf) {
+        """
+        mkdir star
+        touch star/Genome
+        touch star/Log.out
+        touch star/SA
+        touch star/SAindex
+        touch star/chrLength.txt
+        touch star/chrName.txt
+        touch star/chrNameLength.txt
+        touch star/chrStart.txt
+        touch star/exonGeTrInfo.tab
+        touch star/exonInfo.tab
+        touch star/geneInfo.tab
+        touch star/genomeParameters.txt
+        touch star/sjdbInfo.txt
+        touch star/sjdbList.fromGTF.out.tab
+        touch star/sjdbList.out.tab
+        touch star/transcriptInfo.tab
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        star: \$(STAR --version | sed -e "s/STAR_//g")
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-    END_VERSIONS
-    """
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            star: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+        END_VERSIONS
+        """
+    } else {
+        """
+        mkdir star
+        touch star/Genome
+        touch star/Log.out
+        touch star/SA
+        touch star/SAindex
+        touch star/chrLength.txt
+        touch star/chrName.txt
+        touch star/chrNameLength.txt
+        touch star/chrStart.txt
+        touch star/genomeParameters.txt
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            star: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+        END_VERSIONS
+        """
+    }
 }
diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml
index eba2d9cf1..1061e1b8d 100644
--- a/modules/nf-core/star/genomegenerate/meta.yml
+++ b/modules/nf-core/star/genomegenerate/meta.yml
@@ -31,7 +31,6 @@ input:
   - gtf:
       type: file
       description: GTF file of the reference genome
-
 output:
   - meta:
       type: map
@@ -46,7 +45,9 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@kevinmenden"
   - "@drpatelh"
+maintainers:
+  - "@kevinmenden"
+  - "@drpatelh"
diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test
new file mode 100644
index 000000000..fed98212d
--- /dev/null
+++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test
@@ -0,0 +1,110 @@
+nextflow_process {
+
+    name "Test Process STAR_GENOMEGENERATE"
+    script "../main.nf"
+    process "STAR_GENOMEGENERATE"
+
+    test("fasta_gtf") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(),
+                    process.out.versions)
+                .match() }
+            )
+        }
+    }
+
+    test("fasta") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(),
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("fasta_gtf_stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("fasta_stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
new file mode 100644
index 000000000..207f4b4f5
--- /dev/null
+++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
@@ -0,0 +1,148 @@
+{
+    "fasta_gtf": {
+        "content": [
+            "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]",
+            [
+                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:55:35.478401"
+    },
+    "fasta_gtf_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_fasta"
+                        },
+                        [
+                            "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test_fasta"
+                        },
+                        [
+                            "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:55:57.247585"
+    },
+    "fasta_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_fasta"
+                        },
+                        [
+                            "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test_fasta"
+                        },
+                        [
+                            "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:56:07.01742"
+    },
+    "fasta": {
+        "content": [
+            "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]",
+            [
+                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T14:55:45.48784"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml
new file mode 100644
index 000000000..7a0eccdb8
--- /dev/null
+++ b/modules/nf-core/stringtie/stringtie/environment.yml
@@ -0,0 +1,7 @@
+name: stringtie_stringtie
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::stringtie=2.2.1
diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf
index d0f8b563f..6e25ba27d 100644
--- a/modules/nf-core/stringtie/stringtie/main.nf
+++ b/modules/nf-core/stringtie/stringtie/main.nf
@@ -2,7 +2,7 @@ process STRINGTIE_STRINGTIE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::stringtie=2.2.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
         'biocontainers/stringtie:2.2.1--hecb563c_2' }"
diff --git a/modules/nf-core/stringtie/stringtie/meta.yml b/modules/nf-core/stringtie/stringtie/meta.yml
index 75518470b..d8ebdd88a 100644
--- a/modules/nf-core/stringtie/stringtie/meta.yml
+++ b/modules/nf-core/stringtie/stringtie/meta.yml
@@ -5,7 +5,6 @@ keywords:
   - assembly
   - quantification
   - gtf
-
 tools:
   - stringtie2:
       description: |
@@ -55,3 +54,5 @@ output:
       pattern: "versions.yml"
 authors:
   - "@drpatelh"
+maintainers:
+  - "@drpatelh"
diff --git a/modules/nf-core/stringtie/stringtie/nextflow.config b/modules/nf-core/stringtie/stringtie/nextflow.config
new file mode 100644
index 000000000..dc0651458
--- /dev/null
+++ b/modules/nf-core/stringtie/stringtie/nextflow.config
@@ -0,0 +1,17 @@
+if (!params.skip_alignment) {
+    if (!params.skip_stringtie) {
+        process {
+            withName: 'STRINGTIE_STRINGTIE' {
+                ext.args   = { [
+                    '-v',
+                    params.stringtie_ignore_gtf ? '' : '-e'
+                ].join(' ').trim() }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/stringtie" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test
new file mode 100644
index 000000000..dc315a314
--- /dev/null
+++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test
@@ -0,0 +1,209 @@
+nextflow_process {
+
+    name "Test Process STRINGTIE_STRINGTIE"
+    script "../main.nf"
+    process "STRINGTIE_STRINGTIE"
+    config "./nextflow.config"
+
+    test("sarscov2 [bam] - forward strandedness") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', strandedness:'forward' ], // meta map
+                            [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                        ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.abundance,
+                    process.out.transcript_gtf,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - forward strandedness + reference annotation") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', strandedness:'forward' ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                ]
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+                { assert snapshot(
+                    process.out.abundance,
+                    process.out.ballgown,
+                    process.out.transcript_gtf,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - reverse strandedness") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', strandedness:'reverse' ], // meta map
+                            [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                        ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.abundance,
+                    process.out.transcript_gtf,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - reverse strandedness + reference annotation") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', strandedness:'reverse' ], // meta map
+                            [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                        ]
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.abundance,
+                    process.out.ballgown,
+                    process.out.transcript_gtf,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - forward strandedness - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', strandedness:'forward' ], // meta map
+                            [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                        ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - forward strandedness + reference annotation - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', strandedness:'forward' ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                ]
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - reverse strandedness - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', strandedness:'reverse' ], // meta map
+                            [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                        ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - reverse strandedness + reference annotation - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', strandedness:'reverse' ], // meta map
+                            [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+                        ]
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
new file mode 100644
index 000000000..124dd4cbe
--- /dev/null
+++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
@@ -0,0 +1,508 @@
+{
+    "sarscov2 [bam] - forward strandedness + reference annotation": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    [
+                        "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540",
+                        "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471",
+                        "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4",
+                        "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f",
+                        "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04"
+                ]
+            ],
+            [
+                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:33:44.299962"
+    },
+    "sarscov2 [bam] - forward strandedness": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.transcripts.gtf:md5,569137af5be452413086b50653a97203"
+                ]
+            ],
+            [
+                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:33:35.177738"
+    },
+    "sarscov2 [bam] - forward strandedness - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                ],
+                "abundance": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "ballgown": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "coverage_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "transcript_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:36:32.885078"
+    },
+    "sarscov2 [bam] - forward strandedness + reference annotation - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                ],
+                "abundance": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "ballgown": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "coverage_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "transcript_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:36:43.325777"
+    },
+    "sarscov2 [bam] - reverse strandedness + reference annotation - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                ],
+                "abundance": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "ballgown": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "coverage_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "transcript_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:37:06.085936"
+    },
+    "sarscov2 [bam] - reverse strandedness - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                ],
+                "abundance": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "ballgown": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "coverage_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "transcript_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:36:53.837578"
+    },
+    "sarscov2 [bam] - reverse strandedness + reference annotation": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    [
+                        "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540",
+                        "e_data.ctab:md5,879b6696029d19c4737b562e9d149218",
+                        "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4",
+                        "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f",
+                        "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa"
+                ]
+            ],
+            [
+                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:34:03.114695"
+    },
+    "sarscov2 [bam] - reverse strandedness": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "reverse"
+                    },
+                    "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f"
+                ]
+            ],
+            [
+                "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:33:52.874479"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/stringtie/stringtie/tests/nextflow.config b/modules/nf-core/stringtie/stringtie/tests/nextflow.config
new file mode 100644
index 000000000..e3aaa0999
--- /dev/null
+++ b/modules/nf-core/stringtie/stringtie/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'STRINGTIE_STRINGTIE' {
+        ext.args = ''
+    }
+}
diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml
new file mode 100644
index 000000000..ca19439d7
--- /dev/null
+++ b/modules/nf-core/subread/featurecounts/environment.yml
@@ -0,0 +1,7 @@
+name: subread_featurecounts
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::subread=2.0.1
diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf
index a524b92f1..471bd16fd 100644
--- a/modules/nf-core/subread/featurecounts/main.nf
+++ b/modules/nf-core/subread/featurecounts/main.nf
@@ -2,7 +2,7 @@ process SUBREAD_FEATURECOUNTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::subread=2.0.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' :
         'biocontainers/subread:2.0.1--hed695b0_0' }"
@@ -44,4 +44,16 @@ process SUBREAD_FEATURECOUNTS {
         subread: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.featureCounts.txt
+    touch ${prefix}.featureCounts.txt.summary
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        subread: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/subread/featurecounts/meta.yml b/modules/nf-core/subread/featurecounts/meta.yml
index cf02f1ea7..38a379456 100644
--- a/modules/nf-core/subread/featurecounts/meta.yml
+++ b/modules/nf-core/subread/featurecounts/meta.yml
@@ -5,7 +5,6 @@ keywords:
   - fasta
   - genome
   - reference
-
 tools:
   - featurecounts:
       description: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.
@@ -13,7 +12,6 @@ tools:
       documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
       doi: "10.1093/bioinformatics/btt656"
       licence: ["GPL v3"]
-
 input:
   - meta:
       type: map
@@ -28,7 +26,6 @@ input:
       type: file
       description: Genomic features annotation in GTF or SAF
       pattern: "*.{gtf,saf}"
-
 output:
   - meta:
       type: map
@@ -47,6 +44,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@ntoda03"
+maintainers:
+  - "@ntoda03"
diff --git a/modules/nf-core/subread/featurecounts/nextflow.config b/modules/nf-core/subread/featurecounts/nextflow.config
new file mode 100644
index 000000000..3a796d101
--- /dev/null
+++ b/modules/nf-core/subread/featurecounts/nextflow.config
@@ -0,0 +1,26 @@
+if (!params.skip_alignment && !params.skip_qc) {
+    if (!params.skip_biotype_qc && params.featurecounts_group_type) {
+        process {
+            withName: 'SUBREAD_FEATURECOUNTS' {
+                ext.args   = { [
+                    '-B -C',
+                    params.gencode ? "-g gene_type" : "-g $params.featurecounts_group_type",
+                    "-t $params.featurecounts_feature_type"
+                ].join(' ').trim() }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+
+            withName: 'MULTIQC_CUSTOM_BIOTYPE' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+}
diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test b/modules/nf-core/subread/featurecounts/tests/main.nf.test
new file mode 100644
index 000000000..3c0c829bf
--- /dev/null
+++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test
@@ -0,0 +1,151 @@
+nextflow_process {
+
+    name "Test Process SUBREAD_FEATURECOUNTS"
+    script "../main.nf"
+    process "SUBREAD_FEATURECOUNTS"
+    config "./nextflow.config"
+
+    test("sarscov2 [bam] - forward") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true, strandedness:'forward' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.counts).match("forward_counts") },
+                { assert snapshot(process.out.summary).match("forward_summary") },
+                { assert snapshot(process.out.versions).match("forward_versions") }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - forward - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true, strandedness:'forward' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - reverse") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true, strandedness:'reverse' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.counts).match("reverse_counts") },
+                { assert snapshot(process.out.summary).match("reverse_summary") },
+                { assert snapshot(process.out.versions).match("reverse_versions") }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - reverse - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true, strandedness:'reverse' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - unstranded") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.counts).match("unstranded_counts") },
+                { assert snapshot(process.out.summary).match("unstranded_summary") },
+                { assert snapshot(process.out.versions).match("unstranded_versions") }
+            )
+        }
+    }
+
+    test("sarscov2 [bam] - unstranded - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap
new file mode 100644
index 000000000..72e8dcddf
--- /dev/null
+++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap
@@ -0,0 +1,323 @@
+{
+    "forward_counts": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true,
+                        "strandedness": "forward"
+                    },
+                    "test.featureCounts.txt:md5,0012df4c0a0e47eec1440017ab34f75f"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T15:50:10.685863663"
+    },
+    "unstranded_counts": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true,
+                        "strandedness": "unstranded"
+                    },
+                    "test.featureCounts.txt:md5,3307d31b44a5d6bb3389786bb8f4e91f"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T15:50:38.67903701"
+    },
+    "reverse_summary": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true,
+                        "strandedness": "reverse"
+                    },
+                    "test.featureCounts.txt.summary:md5,7cfa30ad678b9bc1bc63afbb0281547b"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T15:50:25.168206514"
+    },
+    "sarscov2 [bam] - forward - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726"
+                ],
+                "counts": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "forward"
+                        },
+                        "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T10:04:22.628032"
+    },
+    "sarscov2 [bam] - reverse - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "reverse"
+                        },
+                        "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "reverse"
+                        },
+                        "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726"
+                ],
+                "counts": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "reverse"
+                        },
+                        "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "reverse"
+                        },
+                        "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T10:04:52.371212"
+    },
+    "reverse_counts": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true,
+                        "strandedness": "reverse"
+                    },
+                    "test.featureCounts.txt:md5,8175816b8260ed444d59232bd7e7120b"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T15:50:25.160010804"
+    },
+    "sarscov2 [bam] - unstranded - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "unstranded"
+                        },
+                        "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "unstranded"
+                        },
+                        "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726"
+                ],
+                "counts": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "unstranded"
+                        },
+                        "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true,
+                            "strandedness": "unstranded"
+                        },
+                        "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T10:05:25.058902"
+    },
+    "forward_summary": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true,
+                        "strandedness": "forward"
+                    },
+                    "test.featureCounts.txt.summary:md5,8f602ff9a8ef467af43294e80b367cdf"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T15:50:10.699024934"
+    },
+    "forward_versions": {
+        "content": [
+            [
+                "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T15:50:10.704797013"
+    },
+    "unstranded_summary": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true,
+                        "strandedness": "unstranded"
+                    },
+                    "test.featureCounts.txt.summary:md5,23164b79f9f23f11c82820db61a35560"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T15:50:38.68776235"
+    },
+    "reverse_versions": {
+        "content": [
+            [
+                "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T15:50:25.175265594"
+    },
+    "unstranded_versions": {
+        "content": [
+            [
+                "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-23T15:50:38.69390501"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/subread/featurecounts/tests/nextflow.config b/modules/nf-core/subread/featurecounts/tests/nextflow.config
new file mode 100644
index 000000000..d9fd4fd57
--- /dev/null
+++ b/modules/nf-core/subread/featurecounts/tests/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: SUBREAD_FEATURECOUNTS {
+        ext.args = '-t CDS'
+    }
+
+}
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml
new file mode 100644
index 000000000..252ace791
--- /dev/null
+++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "summarizedexperiment_summarizedexperiment"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::bioconductor-summarizedexperiment=1.32.0"
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/main.nf b/modules/nf-core/summarizedexperiment/summarizedexperiment/main.nf
new file mode 100644
index 000000000..cc37092fd
--- /dev/null
+++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/main.nf
@@ -0,0 +1,36 @@
+process SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0' :
+        'biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(matrix_files)
+    tuple val(meta2), path(rowdata)
+    tuple val(meta3), path(coldata)
+
+    output:
+    tuple val(meta), path("*.rds")              , emit: rds
+    tuple val(meta), path("*.R_sessionInfo.log"), emit: log
+    path "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'summarizedexperiment.r'
+
+    stub:
+    """
+    touch ${meta.id}.SummarizedExperiment.rds
+    touch ${meta.id}.R_sessionInfo.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bioconductor-summarizedexperiment: \$(Rscript -e "library(SummarizedExperiment); cat(as.character(packageVersion('SummarizedExperiment')))")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml
new file mode 100644
index 000000000..e5118d289
--- /dev/null
+++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml
@@ -0,0 +1,79 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "summarizedexperiment_summarizedexperiment"
+description: |
+  SummarizedExperiment container
+keywords:
+  - gene
+  - transcript
+  - sample
+  - matrix
+  - assay
+tools:
+  - "summarizedexperiment":
+      description: "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples."
+      homepage: "https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html"
+      documentation: "https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html"
+      tool_dev_url: "https://github.com/Bioconductor/SummarizedExperiment"
+      doi: "10.18129/B9.bioc.SummarizedExperiment"
+      licence: ["Artistic-2.0"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole
+        e.g. `[ id:'SRP123456' ]`
+  - matrix_files:
+      type: directory
+      description: |
+        One or more paths to CSV or TSV matrix files. All files must have the
+        same rows and columns.
+      pattern: "*.{csv,tsv}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information related to the species
+        reference from which matrix rows are derived e.g. `[ id:'yeast' ]`
+  - rowdata:
+      type: file
+      description: |
+        Metadata on matrix features. One column must contain all matrix row
+        IDs.
+      pattern: "*.{csv,tsv}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole,
+        as represented by the matrix columns and the sample sheet e.g.
+        `[id:'SRP123456' ]`
+  - coldata:
+      type: file
+      description: |
+        Metadata on matrix columns. One column must contain all matrix column
+        IDs.
+      pattern: "*.{csv,tsv}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole
+        e.g. `[ id:'SRP123456' ]`
+  - rds:
+      type: file
+      description: Serialised SummarizedExperiment object
+      pattern: "*.SummarizedExperiment.rds"
+  - log:
+      type: file
+      description: dump of R SessionInfo
+      pattern: "*.log"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@pinin4fjords"
+maintainers:
+  - "@pinin4fjords"
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r b/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r
new file mode 100644
index 000000000..6c705350a
--- /dev/null
+++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r
@@ -0,0 +1,237 @@
+#!/usr/bin/env Rscript
+
+# Written by Lorena Pantano and revised for flexibility in handling assays
+# Released under the MIT license.
+
+library(SummarizedExperiment)
+
+#' Flexibly read CSV or TSV files
+#'
+#' @param file Input file
+#' @param header Passed to read.delim()
+#' @param row.names Passed to read.delim()
+#'
+#' @return output Data frame
+
+read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = TRUE, stringsAsFactors = FALSE){
+
+    ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1))
+
+    if (ext == "tsv" || ext == "txt") {
+        separator <- "\\t"
+    } else if (ext == "csv") {
+        separator <- ","
+    } else {
+        stop(paste("Unknown separator for", ext))
+    }
+
+    read.delim(
+        file,
+        sep = separator,
+        header = header,
+        row.names = row.names,
+        check.names = check.names,
+        stringsAsFactors = stringsAsFactors
+    )
+}
+
+#' Parse out options from a string without recourse to optparse
+#'
+#' @param x Long-form argument list like --opt1 val1 --opt2 val2
+#'
+#' @return named list of options and values similar to optparse
+
+parse_args <- function(x){
+    args_list <- unlist(strsplit(x, ' ?--')[[1]])[-1]
+    args_vals <- lapply(args_list, function(x) scan(text=x, what='character', quiet = TRUE))
+
+    # Ensure the option vectors are length 2 (key/ value) to catch empty ones
+    args_vals <- lapply(args_vals, function(z){ length(z) <- 2; z})
+
+    parsed_args <- structure(lapply(args_vals, function(x) x[2]), names = lapply(args_vals, function(x) x[1]))
+    parsed_args[! is.na(parsed_args)]
+}
+
+#' Find First Column Containing All Specified Entries
+#'
+#' This function searches through each column of a given data frame to find the
+#' first column that contains all of the specified entries in a vector. If such
+#' a column is found, the name of the column is returned. If no column matches,
+#' the function throws an error.
+#'
+#' @param namesVector A character vector containing the names to be matched.
+#' @param df A data frame within which to search for the column containing all
+#'   names specified in `namesVector`.
+#'
+#' @return The name of the first column in `df` that contains all entries from
+#'   `namesVector`. If no such column exists, the function will throw an error.
+
+findColumnWithAllEntries <- function(namesVector, df) {
+    for (colName in names(df)) {
+        if (all(namesVector %in% df[[colName]])) {
+            return(colName)
+        }
+    }
+    cat(capture.output(print(df)), sep="\n", file=stderr())
+    stop(paste("No column contains all vector entries ", paste(namesVector, collapse = ', ')))
+}
+
+#' Check Matrix Name Uniformity in List
+#'
+#' Verifies if all matrices in a list have identical row and column names.
+#' It returns TRUE if uniformity is found, otherwise FALSE.
+#'
+#' @param matrices List of matrices.
+#' @return Logical indicating uniformity of row and column names.
+#' @keywords matrix
+
+checkRowColNames <- function(matrices) {
+    # Simplify the comparison process
+    allEqual <- function(namesList) {
+        all(sapply(namesList[-1], function(x) identical(x, namesList[[1]])))
+    }
+
+    rowNamesEqual <- allEqual(lapply(matrices, rownames))
+    colNamesEqual <- allEqual(lapply(matrices, colnames))
+
+    if ((! rowNamesEqual) || (! colNamesEqual)){
+        stop("Rows or columns different among input matrices")
+    }
+}
+
+#' Parse Metadata From File
+#'
+#' Reads metadata from a specified file and processes it to handle duplicate
+#' rows by aggregating them into a single row based on a unique identifier.
+#' The function dynamically identifies the appropriate ID column if not specified.
+#' It is designed to be flexible for processing either column (sample) or row (feature) metadata.
+#'
+#' @param metadata_path Character string specifying the path to the metadata file.
+#' @param ids Vector of identifiers (column names or row names) used to match against metadata columns.
+#' @param metadata_id_col Optional; character string specifying the column name in the metadata
+#'        to be used as the unique identifier. If NULL, the function attempts to
+#'        automatically find a suitable column based on `ids`.
+#'
+#' @return A data frame of processed metadata with duplicate rows aggregated, and row names set to the unique identifier.
+
+parse_metadata <- function(metadata_path, ids, metadata_id_col = NULL){
+
+    metadata <- read_delim_flexible(metadata_path, stringsAsFactors = FALSE, header = TRUE)
+    if (is.null(metadata_id_col)){
+        metadata_id_col <- findColumnWithAllEntries(ids, metadata)
+    }
+
+    # Remove any all-NA columns
+    metadata <-  metadata[, colSums(is.na(metadata)) != nrow(metadata)]
+
+    # Allow for duplicate rows by the id column
+    metadata <- aggregate(
+        . ~ metadata[[metadata_id_col]],
+        data = metadata,
+        FUN = function(x) paste(unique(x), collapse = ",")
+    )[,-1]
+
+    rownames(metadata) <- metadata[[metadata_id_col]]
+
+    metadata[ids,, drop=FALSE]
+}
+
+################################################
+################################################
+## Main script starts here                    ##
+################################################
+################################################
+
+# Matrices
+
+args_opt <- parse_args('$task.ext.args')
+matrix_files <- as.list(strsplit('$matrix_files', ' ')[[1]])
+
+if ('assay_names' %in% names(args_opt)){
+    names(matrix_files) <- unlist(strsplit(args_opt[['assay_names']], ',')[[1]])
+}else{
+    names(matrix_files) <- unlist(lapply(matrix_files, tools::file_path_sans_ext))
+}
+
+# Build and verify the main assays list for the summarisedexperiment
+
+assay_list <- lapply(matrix_files, function(m){
+    mat <- read_delim_flexible(m, row.names = 1, stringsAsFactors = FALSE)
+    mat[,sapply(mat, is.numeric), drop = FALSE]
+})
+
+checkRowColNames(assay_list)
+
+# Construct SummarizedExperiment
+se <- SummarizedExperiment(
+    assays = assay_list
+)
+
+# Add column (sample) metadata if provided
+
+if ('$coldata' != ''){
+    coldata <- parse_metadata(
+        metadata_path = '$coldata',
+        ids = colnames(assay_list[[1]]),
+        metadata_id_col = args_opt\$coldata_id_col
+    )
+
+    colData(se) <- DataFrame(coldata)
+}
+
+# Add row (feature) metadata if provided
+
+if ('$rowdata' != ''){
+    rowdata <- parse_metadata(
+        metadata_path = '$rowdata',
+        ids = rownames(assay_list[[1]]),
+        metadata_id_col = args_opt\$rowdata_id_col
+    )
+
+    rowData(se) <- DataFrame(rowdata)
+}
+
+# Write outputs as RDS files
+
+prefix <- tools::file_path_sans_ext(matrix_files[1])
+if ('$task.ext.prefix' != 'null'){
+    prefix = '$task.ext.prefix'
+} else if ('$meta.id' != 'null'){
+    prefix = '$meta.id'
+}
+
+# Save the SummarizedExperiment object
+output_file <- paste0(prefix, ".SummarizedExperiment.rds")
+saveRDS(se, file = output_file)
+
+################################################
+################################################
+## R SESSION INFO                             ##
+################################################
+################################################
+
+sink(paste(prefix, "R_sessionInfo.log", sep = '.'))
+citation("SummarizedExperiment")
+print(sessionInfo())
+sink()
+
+################################################
+################################################
+## VERSIONS FILE                              ##
+################################################
+################################################
+
+r.version <- strsplit(version[['version.string']], ' ')[[1]][3]
+summarizedexperiment.version <- as.character(packageVersion('SummarizedExperiment'))
+
+writeLines(
+    c(
+        '"${task.process}":',
+        paste('    bioconductor-summarizedexperiment:', summarizedexperiment.version)
+    ),
+'versions.yml')
+
+################################################
+################################################
+################################################
+################################################
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test
new file mode 100644
index 000000000..8faa18afb
--- /dev/null
+++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test
@@ -0,0 +1,253 @@
+nextflow_process {
+
+    name "Test Process SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT"
+    script "../main.nf"
+    process "SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT"
+
+    setup {
+
+        run("UNTAR") {
+            script "../../../untar/main.nf"
+            process {
+                """
+                input[0] = [
+                [ id:'test'], // meta map
+                file(params.modules_testdata_base_path + "genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz", checkIfExists: true)
+                ]
+                """
+            }
+        }
+        run("CUSTOM_TX2GENE") { 
+            script "../../../custom/tx2gene/main.nf"
+            process {
+                """
+                input[0] = [
+                [ id:'test'], // meta map
+                file(params.modules_testdata_base_path + "genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf", checkIfExists: true)
+                ]
+                input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[2] = 'kallisto'
+                input[3] = 'gene_id' 
+                input[4] = 'gene_name'
+                """
+            }
+        }
+        run("TXIMETA_TXIMPORT") {
+            script "../../../tximeta/tximport/main.nf"
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+                input[2] = 'kallisto'
+                """
+            }
+        } 
+    }
+
+    test("saccharomyces_cerevisiae - multi_matrix - rowdata - coldata") {
+    
+        config "./multi_matrix.config"
+        
+        when {
+            process {
+                """
+                input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])}
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+		input[2] = [
+                    [ id:'gene'], // meta map
+                    file(params.modules_testdata_base_path + "genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            // Some of the log will vary between conda runs- but top bit should be fine
+            def loglines = path(process.out.log[0][1]).readLines()[0..14]
+
+            assertAll(
+                { assert process.success },
+                { assert snapshot(loglines).md5().match("gene_log_multi_matrix_rowdata_coldata") },
+                { assert snapshot(process.out.versions).match('versions_multi_matrix_rowdata_coldata') }
+            )
+        }
+    }
+    
+    test("saccharomyces_cerevisiae - multi_matrix - rowdata") {
+        
+        config "./multi_matrix.config"
+        
+        when {
+            process {
+                """
+                input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])}
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+                input[2] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            // Some of the log will vary between conda runs- but top bit should be fine
+            def loglines = path(process.out.log[0][1]).readLines()[0..14]
+
+            assertAll(
+                { assert process.success },
+                { assert snapshot(loglines).md5().match("gene_log_multi_matrix_rowdata") },
+                { assert snapshot(process.out.versions).match('versions_multi_matrix_rowdata') }
+            )
+        }
+    }
+    
+    test("saccharomyces_cerevisiae - multi_matrix") {
+        
+        config "./multi_matrix.config"
+        
+        when {
+            process {
+                """
+                input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])}
+                input[1] = Channel.of([ [], [] ])
+                input[2] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            // Some of the log will vary between conda runs- but top bit should be fine
+            def loglines = path(process.out.log[0][1]).readLines()[0..14]
+
+            assertAll(
+                { assert process.success },
+                { assert snapshot(loglines).md5().match("gene_log_multi_matrix") },
+                { assert snapshot(process.out.versions).match('versions_multi_matrix') }
+            )
+        }
+    }
+    
+    test("saccharomyces_cerevisiae - single_matrix") {
+        
+        config "./single_matrix.config"
+        
+        when {
+            process {
+                """
+                input[0] = TXIMETA_TXIMPORT.out.counts_gene
+                input[1] = Channel.of([ [], [] ])
+                input[2] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            // Some of the log will vary between conda runs- but top bit should be fine
+            def loglines = path(process.out.log[0][1]).readLines()[0..14]
+
+            assertAll(
+                { assert process.success },
+                { assert snapshot(loglines).md5().match("gene_log_single_matrix") },
+                { assert snapshot(process.out.versions).match('versions_single_matrix') }
+            )
+        }
+    }
+
+    test("saccharomyces_cerevisiae - multi_matrix - rowdata - coldata - stub") {
+    
+        config "./multi_matrix.config"
+        options "-stub"
+        
+        when {
+            process {
+                """
+                input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])}
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+		input[2] = [
+                    [ id:'gene'], // meta map
+                    file(params.modules_testdata_base_path + "genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.log).match("gene_log_multi_matrix_rowdata_coldataa_stub") },
+                { assert snapshot(process.out.versions).match('versions_multi_matrix_rowdata_coldata_stub') }
+            )
+        }
+    }
+    
+    test("saccharomyces_cerevisiae - multi_matrix - rowdata - stub") {
+        
+        config "./multi_matrix.config"
+        options "-stub"
+        
+        when {
+            process {
+                """
+                input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])}
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+                input[2] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.log).match("gene_log_multi_matrix_rowdata_stub") },
+                { assert snapshot(process.out.versions).match('versions_multi_matrix_rowdata_stub') }
+            )
+        }
+    }
+    
+    test("saccharomyces_cerevisiae - multi_matrix - stub") {
+        
+        config "./multi_matrix.config"
+        options "-stub"
+        
+        when {
+            process {
+                """
+                input[0] = TXIMETA_TXIMPORT.out.counts_gene.join(TXIMETA_TXIMPORT.out.tpm_gene).map{tuple(it[0], [it[1], it[2]])}
+                input[1] = Channel.of([ [], [] ])
+                input[2] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.log).match("gene_log_multi_matrix_stub") },
+                { assert snapshot(process.out.versions).match('versions_multi_matrix_stub') }
+            )
+        }
+    }
+    
+    test("saccharomyces_cerevisiae - single_matrix - stub") {
+        
+        config "./single_matrix.config"
+        options "-stub"
+        
+        when {
+            process {
+                """
+                input[0] = TXIMETA_TXIMPORT.out.counts_gene
+                input[1] = Channel.of([ [], [] ])
+                input[2] = Channel.of([ [], [] ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.log).match("gene_log_single_matrix_stub") },
+                { assert snapshot(process.out.versions).match('versions_single_matrix_stub') }
+            )
+        }
+    }
+}
+
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap
new file mode 100644
index 000000000..1460532c7
--- /dev/null
+++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap
@@ -0,0 +1,198 @@
+{
+    "gene_log_multi_matrix_rowdata_coldataa_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-11T16:41:31.796715"
+    },
+    "gene_log_single_matrix_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-11T16:42:47.12955"
+    },
+    "versions_single_matrix": {
+        "content": [
+            [
+                "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-08T14:45:26.13363"
+    },
+    "gene_log_multi_matrix_rowdata_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-11T16:41:54.028064"
+    },
+    "gene_log_multi_matrix_rowdata": {
+        "content": "7c35131fdd46dcdba6c71f7f11d5b2c7",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-09T14:02:24.430008757"
+    },
+    "versions_multi_matrix_rowdata_stub": {
+        "content": [
+            [
+                "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-11T16:41:54.080728"
+    },
+    "versions_multi_matrix_stub": {
+        "content": [
+            [
+                "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-11T16:42:21.425746"
+    },
+    "versions_multi_matrix_rowdata_coldata_stub": {
+        "content": [
+            [
+                "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-11T16:41:31.837174"
+    },
+    "gene_log_multi_matrix": {
+        "content": "7c35131fdd46dcdba6c71f7f11d5b2c7",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-09T14:02:46.367962336"
+    },
+    "gene_log_multi_matrix_stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-11T16:42:21.370562"
+    },
+    "gene_log_single_matrix": {
+        "content": "7c35131fdd46dcdba6c71f7f11d5b2c7",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-09T14:03:08.330328893"
+    },
+    "versions_single_matrix_stub": {
+        "content": [
+            [
+                "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-11T16:42:47.173221"
+    },
+    "versions_multi_matrix_rowdata": {
+        "content": [
+            [
+                "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-08T14:44:42.420728"
+    },
+    "gene_log_multi_matrix_rowdata_coldata": {
+        "content": "7c35131fdd46dcdba6c71f7f11d5b2c7",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-09T14:02:01.244907114"
+    },
+    "versions_multi_matrix": {
+        "content": [
+            [
+                "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-08T14:45:04.188507"
+    },
+    "versions_multi_matrix_rowdata_coldata": {
+        "content": [
+            [
+                "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-08T14:44:20.698714"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/multi_matrix.config b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/multi_matrix.config
new file mode 100644
index 000000000..5e6d2fc3c
--- /dev/null
+++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/multi_matrix.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT {
+        ext.args = '--assay_names counts,abundance'
+    }
+
+}
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/single_matrix.config b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/single_matrix.config
new file mode 100644
index 000000000..4b6440fd9
--- /dev/null
+++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/single_matrix.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT {
+        ext.args = '--assay_names counts'
+    }
+
+}
diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml
new file mode 100644
index 000000000..0981320c1
--- /dev/null
+++ b/modules/nf-core/trimgalore/environment.yml
@@ -0,0 +1,10 @@
+name: trimgalore
+
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+
+dependencies:
+  - bioconda::cutadapt=3.4
+  - bioconda::trim-galore=0.6.7
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
index dcb77ae7b..0e2f32902 100644
--- a/modules/nf-core/trimgalore/main.nf
+++ b/modules/nf-core/trimgalore/main.nf
@@ -2,7 +2,7 @@ process TRIMGALORE {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::trim-galore=0.6.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' :
         'biocontainers/trim-galore:0.6.7--hdfd78af_0' }"
@@ -72,4 +72,25 @@ process TRIMGALORE {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.single_end) {
+        output_command = "echo '' | gzip > ${prefix}_trimmed.fq.gz ;"
+        output_command += "touch ${prefix}.fastq.gz_trimming_report.txt"
+    } else {
+        output_command = "echo '' | gzip > ${prefix}_1_trimmed.fq.gz ;"
+        output_command += "touch ${prefix}_1.fastq.gz_trimming_report.txt ;"
+        output_command += "echo '' | gzip > ${prefix}_2_trimmed.fq.gz ;"
+        output_command += "touch ${prefix}_2.fastq.gz_trimming_report.txt"
+    }
+    """
+    ${output_command}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
+        cutadapt: \$(cutadapt --version)
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml
index f84c4d771..e649088ce 100644
--- a/modules/nf-core/trimgalore/meta.yml
+++ b/modules/nf-core/trimgalore/meta.yml
@@ -62,3 +62,7 @@ authors:
   - "@drpatelh"
   - "@ewels"
   - "@FelixKrueger"
+maintainers:
+  - "@drpatelh"
+  - "@ewels"
+  - "@FelixKrueger"
diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test
new file mode 100644
index 000000000..4010af8f4
--- /dev/null
+++ b/modules/nf-core/trimgalore/tests/main.nf.test
@@ -0,0 +1,147 @@
+nextflow_process {
+
+    name "Test Process TRIMGALORE"
+    script "../main.nf"
+    process "TRIMGALORE"
+
+    test("test_trimgalore_single_end") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            def read_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1",
+								"TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT",
+								"AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA",
+								"@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1",
+								"ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC",
+								"AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"]
+            def report1_lines = ["1	19	25.0	0	19",
+                                    "2	10	6.2	0	10",
+                                    "3	1	1.6	0	1"]
+            assertAll(
+                { assert process.success },
+                { read_lines.each { read_line ->
+                    { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) }
+                    }
+                },
+                { report1_lines.each { report1_line ->
+                    { assert path(process.out.log.get(0).get(1)).getText().contains(report1_line) }
+                    }
+                },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_trimgalore_single_end - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_trimgalore_paired_end") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1",
+									"TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT",
+									"AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA",
+									"@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1",
+									"ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC",
+									"AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"]
+            def read2_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2",
+									"ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG",
+									"AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE",
+									"@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/2",
+									"GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT",
+									"AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE"]
+            def report1_lines = ["1	19	25.0	0	19",
+                                    "2	10	6.2	0	10",
+                                    "3	1	1.6	0	1"]
+            def report2_lines = ["1	28	25.0	0	28",
+                                    "2	10	6.2	0	10",
+                                    "3	1	1.6	0	1"]
+            assertAll(
+                { assert process.success },
+                { read1_lines.each { read1_line ->
+                    { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) }
+                    }
+                },
+                { read2_lines.each { read2_line ->
+                    { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) }
+                    }
+                },
+                { report1_lines.each { report1_line ->
+                    { assert path(process.out.log.get(0).get(1).get(0)).getText().contains(report1_line) }
+                    }
+                },
+                { report2_lines.each { report2_line ->
+                    { assert path(process.out.log.get(0).get(1).get(1)).getText().contains(report2_line) }
+                    }
+                },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_trimgalore_paired_end - stub") {
+
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap
new file mode 100644
index 000000000..6cb31c9f9
--- /dev/null
+++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap
@@ -0,0 +1,180 @@
+{
+    "test_trimgalore_single_end": {
+        "content": [
+            [
+                "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-29T16:33:20.401347"
+    },
+    "test_trimgalore_single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7"
+                ],
+                "html": [
+                    
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "unpaired": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7"
+                ],
+                "zip": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T10:27:44.964166"
+    },
+    "test_trimgalore_paired_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7"
+                ],
+                "html": [
+                    
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "unpaired": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7"
+                ],
+                "zip": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T10:28:07.611496"
+    },
+    "test_trimgalore_paired_end": {
+        "content": [
+            [
+                "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-02-29T16:33:28.960497"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml
new file mode 100644
index 000000000..24b202222
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "tximeta_tximport"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::bioconductor-tximeta=1.20.1"
diff --git a/modules/nf-core/tximeta/tximport/main.nf b/modules/nf-core/tximeta/tximport/main.nf
new file mode 100644
index 000000000..b0cce8536
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/main.nf
@@ -0,0 +1,47 @@
+process TXIMETA_TXIMPORT {
+    label "process_medium"
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bioconductor-tximeta%3A1.20.1--r43hdfd78af_0' :
+        'biocontainers/bioconductor-tximeta:1.20.1--r43hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path("quants/*")
+    tuple val(meta2), path(tx2gene)
+    val quant_type
+
+    output:
+    tuple val(meta), path("*gene_tpm.tsv")                 , emit: tpm_gene
+    tuple val(meta), path("*gene_counts.tsv")              , emit: counts_gene
+    tuple val(meta), path("*gene_counts_length_scaled.tsv"), emit: counts_gene_length_scaled
+    tuple val(meta), path("*gene_counts_scaled.tsv")       , emit: counts_gene_scaled
+    tuple val(meta), path("*gene_lengths.tsv")             , emit: lengths_gene
+    tuple val(meta), path("*transcript_tpm.tsv")           , emit: tpm_transcript
+    tuple val(meta), path("*transcript_counts.tsv")        , emit: counts_transcript
+    tuple val(meta), path("*transcript_lengths.tsv")       , emit: lengths_transcript
+    path "versions.yml"                                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'tximport.r'
+
+    stub:
+    """
+    touch ${meta.id}.gene_tpm.tsv
+    touch ${meta.id}.gene_counts.tsv
+    touch ${meta.id}.gene_counts_length_scaled.tsv
+    touch ${meta.id}.gene_counts_scaled.tsv
+    touch ${meta.id}.gene_lengths.tsv
+    touch ${meta.id}.transcript_tpm.tsv
+    touch ${meta.id}.transcript_counts.tsv
+    touch ${meta.id}.transcript_lengths.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bioconductor-tximeta: \$(Rscript -e "library(tximeta); cat(as.character(packageVersion('tximeta')))")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/tximeta/tximport/meta.yml b/modules/nf-core/tximeta/tximport/meta.yml
new file mode 100644
index 000000000..9ee5fd365
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/meta.yml
@@ -0,0 +1,120 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "tximeta_tximport"
+description: |
+  Import transcript-level abundances and estimated counts for gene-level
+  analysis packages
+keywords:
+  - gene
+  - kallisto
+  - pseudoalignment
+  - salmon
+  - transcript
+tools:
+  - "tximeta":
+      description: "Transcript Quantification Import with Automatic Metadata"
+      homepage: "https://bioconductor.org/packages/release/bioc/html/tximeta.html"
+      documentation: "https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.html"
+      tool_dev_url: "https://github.com/thelovelab/tximeta"
+      doi: "10.1371/journal.pcbi.1007664"
+      licence: ["GPL-2"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole
+        e.g. `[ id:'SRP123456' ]`
+  - quants:
+      type: directory
+      description: Paths to subdirectories corresponding to
+        sample-wise runs of Salmon or Kallisto
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information related to the species
+        reference e.g. `[ id:'yeast' ]`
+  - tx2gene:
+      type: file
+      description: A transcript to gene mapping table such as those generated
+        by custom/tx2gene
+      pattern: "*.{csv,tsv}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole
+        e.g. `[ id:'SRP123456' ]`
+  - coldata:
+      type: file
+      description: |
+        Optional 'coldata' file equivalent to a sample sheet where the first
+        column corresponds to the sample names (directory names in the input
+        salmon/ kallisto results)
+      pattern: "*.{csv,tsv}"
+  - quant_type:
+      type: string
+      description: Quantification type, 'kallisto' or 'salmon'
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole
+        e.g. `[ id:'SRP123456' ]`
+  - tpm_gene:
+      type: file
+      description: |
+        Abundance (TPM) values derived from tximport output after
+        summarizeToGene(), without a 'countsFromAbundance' specification
+      pattern: "*gene_tpm.tsv"
+  - counts_gene:
+      type: file
+      description: |
+        Count values derived from tximport output after
+        summarizeToGene(), without a 'countsFromAbundance' specification
+      pattern: "*gene_counts.tsv"
+  - counts_gene_length_scaled:
+      type: file
+      description: |
+        Count values derived from tximport output after summarizeToGene(), with
+        a 'countsFromAbundance' specification of 'lengthScaledTPM'
+      pattern: "*gene_counts_length_scaled.tsv"
+  - counts_gene_scaled:
+      type: file
+      description: |
+        Count values derived from tximport output after summarizeToGene(), with
+        a 'countsFromAbundance' specification of 'scaledTPM'
+      pattern: "*gene_counts_scaled.tsv"
+  - lengths_gene:
+      type: file
+      description: |
+        Length values derived from tximport output after summarizeToGene(),
+        without a 'countsFromAbundance' specification
+      pattern: "*gene_lengths.tsv"
+  - tpm_transcript:
+      type: file
+      description: |
+        Abundance (TPM) values derived from tximport output without
+        summarizeToGene(), without a 'countsFromAbundance' specification
+      pattern: "*transcript_tpm.tsv"
+  - counts_transcript:
+      type: file
+      description: |
+        Count values derived from tximport output without
+        summarizeToGene(), without a 'countsFromAbundance' specification
+      pattern: "*transcript_counts.tsv"
+  - lengths_transcript:
+      type: file
+      description: |
+        Length values derived from tximport output without summarizeToGene(),
+        without a 'countsFromAbundance' specification
+      pattern: "*gene_lengths.tsv"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@pinin4fjords"
+maintainers:
+  - "@pinin4fjords"
diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r
new file mode 100755
index 000000000..e8235c8b0
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/templates/tximport.r
@@ -0,0 +1,217 @@
+#!/usr/bin/env Rscript --vanilla
+
+# Script for importing and processing transcript-level quantifications.
+# Written by Lorena Pantano, later modified by Jonathan Manning, and released
+# under the MIT license.
+
+# Loading required libraries
+library(SummarizedExperiment)
+library(tximport)
+
+################################################
+################################################
+## Functions                                  ##
+################################################
+################################################
+
+#' Build a table from a SummarizedExperiment object
+#'
+#' This function takes a SummarizedExperiment object and a specific slot name to extract
+#' assay data. It then combines the first two columns of the rowData with the specified
+#' assay data slot into a new data table.
+#'
+#' @param se.obj A SummarizedExperiment object from which to build the table.
+#' @param slot The name of the slot in the assays list from which to extract data.
+#'
+#' @return A data frame combining the first two columns of the rowData with the assay data from the specified slot.
+
+build_table <- function(se.obj, slot) {
+    cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]])
+}
+
+#' Write a table to a file from a SummarizedExperiment object with given parameters
+#'
+#' This function generates a table from a SummarizedExperiment object using specified parameters
+#' and writes the resulting table to a file. The file name is constructed using a prefix and a
+#' suffix from the parameters, and the table is written with tab separation, without quoting text,
+#' and without row names.
+#'
+#' @param params A list containing the parameters needed for file generation and table writing.
+#' The list should include:
+#' - `obj`: A SummarizedExperiment object from which to build the table.
+#' - `slot`: The name of the slot in the assays list from which to extract data.
+#' - `suffix`: Suffix to use for generating the file name.
+#'
+#' @return NULL The function is called for its side effect of writing a file and does not return anything.
+
+write_se_table <- function(params, prefix) {
+    file_name <- paste0(prefix, ".", params\$suffix)
+    write.table(build_table(params\$obj, params\$slot), file_name,
+                sep="\t", quote=FALSE, row.names = FALSE)
+}
+
+#' Read Transcript Metadata from a Given Path
+#'
+#' This function reads transcript metadata from a specified file path. The file is expected to
+#' be a tab-separated values file without headers, containing transcript information. The function
+#' checks if the file is empty and stops execution with an error message if so. It reads the file
+#' into a data frame, expecting columns for transcript IDs, gene IDs, and gene names. Additional
+#' processing is done to ensure compatibility with a predefined data structure (e.g., `txi[[1]]`),
+#' including adding missing entries and reordering based on the transcript IDs found in `txi[[1]]`.
+#'
+#' @param tinfo_path The file path to the transcript information file.
+#'
+#' @return A list containing three elements:
+#' - `transcript`: A data frame with transcript IDs, gene IDs, and gene names, indexed by transcript IDs.
+#' - `gene`: A data frame with unique gene IDs and gene names.
+#' - `tx2gene`: A data frame mapping transcript IDs to gene IDs.
+
+read_transcript_info <- function(tinfo_path){
+    info <- file.info(tinfo_path)
+    if (info\$size == 0) {
+        stop("tx2gene file is empty")
+    }
+
+    transcript_info <- read.csv(tinfo_path, sep="\t", header = TRUE,
+                                col.names = c("tx", "gene_id", "gene_name"))
+
+    extra <- setdiff(rownames(txi[[1]]), as.character(transcript_info[["tx"]]))
+    transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra))
+    transcript_info <- transcript_info[match(rownames(txi[[1]]), transcript_info[["tx"]]), ]
+    rownames(transcript_info) <- transcript_info[["tx"]]
+
+    list(transcript = transcript_info,
+        gene = unique(transcript_info[,2:3]),
+        tx2gene = transcript_info[,1:2])
+}
+
+#' Create a SummarizedExperiment Object
+#'
+#' Constructs a SummarizedExperiment object using provided matrices for counts, abundance, and length,
+#' along with metadata for columns and rows. This function facilitates the organization of experimental
+#' data (e.g., RNA-seq or other high-throughput data) in a structured format that is convenient for
+#' further analyses and visualization.
+#'
+#' @param counts A matrix or DataFrame containing counts data, with rows as features (e.g., genes) and
+#' columns as samples.
+#' @param abundance A matrix or DataFrame containing abundance data (e.g., TPM or FPKM) with the same
+#' dimensions and row/column names as the counts data.
+#' @param length A matrix or DataFrame containing feature lengths, matching the dimensions and row/column
+#' names of the counts data.
+#' @param col_data A DataFrame containing sample-level metadata, with rows corresponding to columns in the
+#' counts, abundance, and length matrices.
+#' @param row_data A DataFrame containing feature-level metadata, with rows corresponding to features in
+#' the counts, abundance, and length matrices.
+#'
+#' @return A SummarizedExperiment object containing the supplied data and metadata.
+
+create_summarized_experiment <- function(counts, abundance, length, col_data, row_data) {
+    SummarizedExperiment(assays = list(counts = counts, abundance = abundance, length = length),
+        colData = col_data,
+        rowData = row_data)
+}
+
+################################################
+################################################
+## Main script starts here                    ##
+################################################
+################################################
+
+# Define pattern for file names based on quantification type
+pattern <- ifelse('$quant_type' == "kallisto", "abundance.tsv", "quant.sf")
+fns <- list.files('quants', pattern = pattern, recursive = T, full.names = T)
+names <- basename(dirname(fns))
+names(fns) <- names
+dropInfReps <- '$quant_type' == "kallisto"
+
+# Import transcript-level quantifications
+txi <- tximport(fns, type = '$quant_type', txOut = TRUE, dropInfReps = dropInfReps)
+
+# Read transcript and sample data
+transcript_info <- read_transcript_info('$tx2gene')
+
+# Make coldata just to appease the summarizedexperiment
+coldata <- data.frame(files = fns, names = names)
+rownames(coldata) <- coldata[["names"]]
+
+# Create initial SummarizedExperiment object
+se <- create_summarized_experiment(txi[["counts"]], txi[["abundance"]], txi[["length"]],
+    DataFrame(coldata), transcript_info\$transcript)
+
+# Setting parameters for writing tables
+params <- list(
+    list(obj = se, slot = "abundance", suffix = "transcript_tpm.tsv"),
+    list(obj = se, slot = "counts", suffix = "transcript_counts.tsv"),
+    list(obj = se, slot = "length", suffix = "transcript_lengths.tsv")
+)
+
+# Process gene-level data if tx2gene mapping is available
+if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info\$tx2gene)) {
+    tx2gene <- transcript_info\$tx2gene
+    gi <- summarizeToGene(txi, tx2gene = tx2gene)
+    gi.ls <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM")
+    gi.s <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "scaledTPM")
+
+    gene_info <- transcript_info\$gene[match(rownames(gi[[1]]), transcript_info\$gene[["gene_id"]]),]
+    rownames(gene_info) <- NULL
+    col_data_frame <- DataFrame(coldata)
+
+    # Create gene-level SummarizedExperiment objects
+    gse <- create_summarized_experiment(gi[["counts"]], gi[["abundance"]], gi[["length"]],
+        col_data_frame, gene_info)
+    gse.ls <- create_summarized_experiment(gi.ls[["counts"]], gi.ls[["abundance"]], gi.ls[["length"]],
+        col_data_frame, gene_info)
+    gse.s <- create_summarized_experiment(gi.s[["counts"]], gi.s[["abundance"]], gi.s[["length"]],
+        col_data_frame, gene_info)
+
+    params <- c(params, list(
+        list(obj = gse, slot = "length", suffix = "gene_lengths.tsv"),
+        list(obj = gse, slot = "abundance", suffix = "gene_tpm.tsv"),
+        list(obj = gse, slot = "counts", suffix = "gene_counts.tsv"),
+        list(obj = gse.ls, slot = "counts", suffix = "gene_counts_length_scaled.tsv"),
+        list(obj = gse.s, slot = "counts", suffix = "gene_counts_scaled.tsv")
+    ))
+}
+
+# Writing tables for each set of parameters
+
+prefix <- ''
+if ('$task.ext.prefix' != 'null'){
+    prefix = '$task.ext.prefix'
+} else if ('$meta.id' != 'null'){
+    prefix = '$meta.id'
+}
+
+done <- lapply(params, write_se_table, prefix)
+
+################################################
+################################################
+## R SESSION INFO                             ##
+################################################
+################################################
+
+sink(paste(prefix, "R_sessionInfo.log", sep = '.'))
+citation("tximeta")
+print(sessionInfo())
+sink()
+
+################################################
+################################################
+## VERSIONS FILE                              ##
+################################################
+################################################
+
+r.version <- strsplit(version[['version.string']], ' ')[[1]][3]
+tximeta.version <- as.character(packageVersion('tximeta'))
+
+writeLines(
+    c(
+        '"${task.process}":',
+        paste('    bioconductor-tximeta:', tximeta.version)
+    ),
+'versions.yml')
+
+################################################
+################################################
+################################################
+################################################
diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test
new file mode 100644
index 000000000..782030fb8
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test
@@ -0,0 +1,186 @@
+nextflow_process {
+
+    name "Test Process TXIMETA_TXIMPORT"
+    script "../main.nf"
+    process "TXIMETA_TXIMPORT"
+
+    test("saccharomyces_cerevisiae - kallisto - gtf") {
+
+        setup {
+
+            run("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test'], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+            run("CUSTOM_TX2GENE") {
+                script "../../../custom/tx2gene/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test'], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true)
+                    ])
+                    input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                    input[2] = 'kallisto'
+                    input[3] = 'gene_id'
+                    input[4] = 'gene_name'
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+                input[2] = 'kallisto'
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.counts_gene).match('counts_gene_kallisto') },
+                { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_kallisto') },
+                { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_kallisto') },
+                { assert snapshot(process.out.counts_transcript).match('counts_transcript_kallisto') },
+                { assert snapshot(process.out.lengths_gene).match('lengths_gene_kallisto') },
+                { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_kallisto') },
+                { assert snapshot(process.out.tpm_gene).match('tpm_gene_kallisto') },
+                { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_kallisto') },
+                { assert snapshot(process.out.versions).match('versions_kallisto') }
+            )
+        }
+    }
+
+    test("saccharomyces_cerevisiae - kallisto - gtf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([ [], [] ])
+                input[1] = Channel.of([ [], [] ])
+                input[2] = 'kallisto'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.counts_gene).match('counts_gene_kallisto - stub') },
+                { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_kallisto - stub') },
+                { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_kallisto - stub') },
+                { assert snapshot(process.out.counts_transcript).match('counts_transcript_kallisto - stub') },
+                { assert snapshot(process.out.lengths_gene).match('lengths_gene_kallisto - stub') },
+                { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_kallisto - stub') },
+                { assert snapshot(process.out.tpm_gene).match('tpm_gene_kallisto - stub') },
+                { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_kallisto - stub') },
+                { assert snapshot(process.out.versions).match('versions_kallisto - stub') }
+            )
+        }
+
+    }
+    test("saccharomyces_cerevisiae - salmon - gtf") {
+
+        setup {
+
+            run("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test'], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz', checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+            run("CUSTOM_TX2GENE") {
+                script "../../../custom/tx2gene/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test'], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true)
+                    ])
+                    input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                    input[2] = 'salmon'
+                    input[3] = 'gene_id'
+                    input[4] = 'gene_name'
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+                input[2] = 'salmon'
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.counts_gene).match('counts_gene_salmon') },
+                { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_salmon') },
+                { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_salmon') },
+                { assert snapshot(process.out.counts_transcript).match('counts_transcript_salmon') },
+                { assert snapshot(process.out.lengths_gene).match('lengths_gene_salmon') },
+                { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_salmon') },
+                { assert snapshot(process.out.tpm_gene).match('tpm_gene_salmon') },
+                { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_salmon') },
+                { assert snapshot(process.out.versions).match('versions_salmon') }
+            )
+        }
+
+    }
+
+    test("saccharomyces_cerevisiae - salmon - gtf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([ [], [] ])
+                input[1] = Channel.of([ [], [] ])
+                input[2] = 'salmon'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.counts_gene).match('counts_gene_salmon - stub') },
+                { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_salmon - stub') },
+                { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_salmon - stub') },
+                { assert snapshot(process.out.counts_transcript).match('counts_transcript_salmon - stub') },
+                { assert snapshot(process.out.lengths_gene).match('lengths_gene_salmon - stub') },
+                { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_salmon - stub') },
+                { assert snapshot(process.out.tpm_gene).match('tpm_gene_salmon - stub') },
+                { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_salmon - stub') },
+                { assert snapshot(process.out.versions).match('versions_salmon - stub') }
+            )
+        }
+    }
+}
+
diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap
new file mode 100644
index 000000000..3cd0ee9e4
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap
@@ -0,0 +1,594 @@
+{
+    "tpm_transcript_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:50.683744"
+    },
+    "lengths_gene_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:16.126128"
+    },
+    "counts_gene_scaled_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:50.654405"
+    },
+    "counts_gene_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:16.112898"
+    },
+    "lengths_transcript_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:50.67148"
+    },
+    "versions_salmon - stub": {
+        "content": [
+            [
+                "versions.yml:md5,6ff317cceddc686f84d79cb976e1e28b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:50.690592"
+    },
+    "counts_gene_length_scaled_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_length_scaled.tsv:md5,4944841ac711124d29673b6b6ed16ef3"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:34:59.621599"
+    },
+    "lengths_transcript_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_lengths.tsv:md5,db6d8ab9f8e1123d5984fd534b4347dc"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:32.876208"
+    },
+    "counts_transcript_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_counts.tsv:md5,42e0106e75fa97c1c684c6d9060f1724"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:34:59.62725"
+    },
+    "counts_transcript_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:16.122852"
+    },
+    "counts_transcript_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:32.866731"
+    },
+    "lengths_gene_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:50.6654"
+    },
+    "tpm_gene_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_tpm.tsv:md5,6076364cc78741a4f8bc8935a045d13d"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:32.881193"
+    },
+    "tpm_transcript_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_tpm.tsv:md5,7a334b565e1e865efb1caf615f194ef7"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:32.886363"
+    },
+    "tpm_gene_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:50.677538"
+    },
+    "lengths_transcript_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_lengths.tsv:md5,f974b52840431a5dae57bcb615badbf1"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:34:59.632822"
+    },
+    "counts_gene_length_scaled_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:16.11652"
+    },
+    "tpm_gene_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:16.133742"
+    },
+    "counts_transcript_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:50.660144"
+    },
+    "counts_gene_scaled_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_scaled.tsv:md5,39d14e361434978b3cadae901a26a028"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:34:59.624732"
+    },
+    "counts_gene_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:32.852188"
+    },
+    "versions_salmon": {
+        "content": [
+            [
+                "versions.yml:md5,6ff317cceddc686f84d79cb976e1e28b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:32.892224"
+    },
+    "counts_gene_length_scaled_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_length_scaled.tsv:md5,5f92a6784f6edc5e3b336c71c3ee7daf"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:32.857451"
+    },
+    "tpm_gene_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_tpm.tsv:md5,85d108269769ae0d841247b9b9ed922d"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:34:59.636454"
+    },
+    "lengths_transcript_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:16.129712"
+    },
+    "lengths_gene_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_lengths.tsv:md5,db6becdf807fd164a9c63dd1dd916d9c"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:34:59.630042"
+    },
+    "counts_gene_scaled_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:16.119638"
+    },
+    "tpm_transcript_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_tpm.tsv:md5,65862ed9d4a05abfab952e680dc0e49d"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:34:59.639525"
+    },
+    "lengths_gene_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_lengths.tsv:md5,1691ea2677612805cd699265c83024d7"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:32.871162"
+    },
+    "counts_gene_length_scaled_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:50.605613"
+    },
+    "counts_gene_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts.tsv:md5,e89c28692ea214396b2d4cb702a804c3"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:34:59.61832"
+    },
+    "versions_kallisto": {
+        "content": [
+            [
+                "versions.yml:md5,6ff317cceddc686f84d79cb976e1e28b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:34:59.642751"
+    },
+    "counts_gene_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:50.598457"
+    },
+    "versions_kallisto - stub": {
+        "content": [
+            [
+                "versions.yml:md5,6ff317cceddc686f84d79cb976e1e28b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:16.141689"
+    },
+    "tpm_transcript_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:16.137716"
+    },
+    "counts_gene_scaled_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_scaled.tsv:md5,fdfb3d23aaf5d4316d81247ec4664ca0"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-28T12:35:32.862272"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml
new file mode 100644
index 000000000..571dc2749
--- /dev/null
+++ b/modules/nf-core/ucsc/bedclip/environment.yml
@@ -0,0 +1,7 @@
+name: ucsc_bedclip
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::ucsc-bedclip=377
diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf
index 4bad9a399..d3e09dc11 100755
--- a/modules/nf-core/ucsc/bedclip/main.nf
+++ b/modules/nf-core/ucsc/bedclip/main.nf
@@ -3,7 +3,7 @@ process UCSC_BEDCLIP {
     label 'process_medium'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::ucsc-bedclip=377"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2' :
         'biocontainers/ucsc-bedclip:377--h0b8a92a_2' }"
@@ -34,4 +34,16 @@ process UCSC_BEDCLIP {
         ucsc: $VERSION
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.bedGraph
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ucsc: $VERSION
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/ucsc/bedclip/meta.yml b/modules/nf-core/ucsc/bedclip/meta.yml
old mode 100755
new mode 100644
index cc5d9d715..2467a28f2
--- a/modules/nf-core/ucsc/bedclip/meta.yml
+++ b/modules/nf-core/ucsc/bedclip/meta.yml
@@ -9,7 +9,6 @@ tools:
       description: Remove lines from bed file that refer to off-chromosome locations.
       homepage: http://hgdownload.cse.ucsc.edu/admin/exe/
       licence: ["varies; see http://genome.ucsc.edu/license"]
-
 input:
   - meta:
       type: map
@@ -20,7 +19,6 @@ input:
       type: file
       description: bedGraph file
       pattern: "*.{bedgraph}"
-
 output:
   - meta:
       type: map
@@ -35,6 +33,7 @@ output:
       type: file
       description: bedGraph file
       pattern: "*.{bedgraph}"
-
 authors:
   - "@drpatelh"
+maintainers:
+  - "@drpatelh"
diff --git a/modules/nf-core/ucsc/bedclip/tests/main.nf.test b/modules/nf-core/ucsc/bedclip/tests/main.nf.test
new file mode 100644
index 000000000..5cb8600c3
--- /dev/null
+++ b/modules/nf-core/ucsc/bedclip/tests/main.nf.test
@@ -0,0 +1,53 @@
+nextflow_process {
+
+    name "Test Process UCSC_BEDCLIP"
+    script "../main.nf"
+    process "UCSC_BEDCLIP"
+
+    test("sarscov2") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bedgraph/test.bedgraph", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.sizes", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - stub") {
+        config "./nextflow.config"
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bedgraph/test.bedgraph", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.sizes", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/ucsc/bedclip/tests/main.nf.test.snap b/modules/nf-core/ucsc/bedclip/tests/main.nf.test.snap
new file mode 100644
index 000000000..77e893808
--- /dev/null
+++ b/modules/nf-core/ucsc/bedclip/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "sarscov2 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.clip.bedGraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b92248ce2a138ad4d146ac0d9e71fb34"
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.clip.bedGraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b92248ce2a138ad4d146ac0d9e71fb34"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T10:31:42.86304"
+    },
+    "sarscov2": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.clip.bedGraph:md5,e02395e1f7c593b3f79563067159ebc2"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b92248ce2a138ad4d146ac0d9e71fb34"
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.clip.bedGraph:md5,e02395e1f7c593b3f79563067159ebc2"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b92248ce2a138ad4d146ac0d9e71fb34"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-07T16:04:04.165478"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/ucsc/bedclip/tests/nextflow.config b/modules/nf-core/ucsc/bedclip/tests/nextflow.config
new file mode 100644
index 000000000..13bce9a82
--- /dev/null
+++ b/modules/nf-core/ucsc/bedclip/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: UCSC_BEDCLIP {
+        ext.prefix = { "${meta.id}.clip" }
+    }
+
+}
diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml
new file mode 100644
index 000000000..f91e216f5
--- /dev/null
+++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml
@@ -0,0 +1,7 @@
+name: ucsc_bedgraphtobigwig
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::ucsc-bedgraphtobigwig=445
diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
index 06bb47099..bff0b00a9 100644
--- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
+++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
@@ -3,7 +3,7 @@ process UCSC_BEDGRAPHTOBIGWIG {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::ucsc-bedgraphtobigwig=445"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:445--h954228d_0' :
         'biocontainers/ucsc-bedgraphtobigwig:445--h954228d_0' }"
diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml
index 416c91e07..a60118abe 100755
--- a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml
+++ b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml
@@ -12,7 +12,6 @@ tools:
       homepage: http://hgdownload.cse.ucsc.edu/admin/exe/
       documentation: https://genome.ucsc.edu/goldenPath/help/bigWig.html
       licence: ["varies; see http://genome.ucsc.edu/license"]
-
 input:
   - meta:
       type: map
@@ -27,7 +26,6 @@ input:
       type: file
       description: chromosome sizes file
       pattern: "*.{sizes}"
-
 output:
   - meta:
       type: map
@@ -42,6 +40,7 @@ output:
       type: file
       description: bigWig file
       pattern: "*.{bigWig}"
-
 authors:
   - "@drpatelh"
+maintainers:
+  - "@drpatelh"
diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test
new file mode 100644
index 000000000..d5dbe4a37
--- /dev/null
+++ b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test
@@ -0,0 +1,49 @@
+nextflow_process {
+
+    name "Test Process UCSC_BEDGRAPHTOBIGWIG"
+    script "../main.nf"
+    process "UCSC_BEDGRAPHTOBIGWIG"
+
+    test("Should run without failures") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bedgraph/test.bedgraph", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.sizes", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bedgraph/test.bedgraph", checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.sizes", checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap
new file mode 100644
index 000000000..7b0181583
--- /dev/null
+++ b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bigWig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,93b027527145a243903a3c687c3453b8"
+                ],
+                "bigwig": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bigWig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,93b027527145a243903a3c687c3453b8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:06:05.176746"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bigWig:md5,910ecc7f57e3bbd5fac5a8edba4f615d"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,93b027527145a243903a3c687c3453b8"
+                ],
+                "bigwig": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bigWig:md5,910ecc7f57e3bbd5fac5a8edba4f615d"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,93b027527145a243903a3c687c3453b8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:05:56.658148"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml
new file mode 100644
index 000000000..bc497824f
--- /dev/null
+++ b/modules/nf-core/umitools/dedup/environment.yml
@@ -0,0 +1,7 @@
+name: umitools_dedup
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::umi_tools=1.1.5
diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf
index 824ebeeb3..1e2a2aae0 100644
--- a/modules/nf-core/umitools/dedup/main.nf
+++ b/modules/nf-core/umitools/dedup/main.nf
@@ -2,10 +2,10 @@ process UMITOOLS_DEDUP {
     tag "$meta.id"
     label "process_medium"
 
-    conda "bioconda::umi_tools=1.1.4"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/umi_tools:1.1.4--py38hbff2b2d_1' :
-        'biocontainers/umi_tools:1.1.4--py38hbff2b2d_1' }"
+        'https://depot.galaxyproject.org/singularity/umi_tools:1.1.5--py39hf95cd2a_0' :
+        'biocontainers/umi_tools:1.1.5--py39hf95cd2a_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -47,6 +47,7 @@ process UMITOOLS_DEDUP {
     """
 
     stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam
     touch ${prefix}.log
diff --git a/modules/nf-core/umitools/dedup/meta.yml b/modules/nf-core/umitools/dedup/meta.yml
index 534d4c6b0..38d3fd465 100644
--- a/modules/nf-core/umitools/dedup/meta.yml
+++ b/modules/nf-core/umitools/dedup/meta.yml
@@ -7,8 +7,8 @@ keywords:
 tools:
   - umi_tools:
       description: >
-        UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
-        and single cell RNA-Seq cell barcodes
+        UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
+
       documentation: https://umi-tools.readthedocs.io/en/latest/
       license: ["MIT"]
 input:
@@ -61,8 +61,11 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@drpatelh"
   - "@grst"
   - "@klkeys"
+maintainers:
+  - "@drpatelh"
+  - "@grst"
+  - "@klkeys"
diff --git a/modules/nf-core/umitools/dedup/tests/main.nf.test b/modules/nf-core/umitools/dedup/tests/main.nf.test
new file mode 100644
index 000000000..883e2d9d7
--- /dev/null
+++ b/modules/nf-core/umitools/dedup/tests/main.nf.test
@@ -0,0 +1,183 @@
+nextflow_process {
+
+    name "Test Process UMITOOLS_DEDUP"
+    script "../main.nf"
+    process "UMITOOLS_DEDUP"
+
+    test("se - no stats") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                get_output_stats = false
+
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai", checkIfExists: true)
+                ]
+                input[1] = get_output_stats
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path("${process.out.log[0][1]}").exists() },
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getSamLinesMD5(),
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("pe - no stats") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                get_output_stats = false
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ]
+                input[1] = get_output_stats
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path("${process.out.log[0][1]}").exists() },
+                { assert snapshot(
+                    process.out.bam,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("pe - with stats") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                get_output_stats = true
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ]
+                input[1] = get_output_stats
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path("${process.out.log[0][1]}").exists() },
+                { assert snapshot(
+                    process.out.bam,
+                    process.out.tsv_edit_distance,
+                    process.out.tsv_per_umi,
+                    process.out.tsv_umi_per_position,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+    test("se - no stats - stub") {
+
+        options "-stub"
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                get_output_stats = false
+
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai", checkIfExists: true)
+                ]
+                input[1] = get_output_stats
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.bam).match() }
+            )
+        }
+    }
+
+    test("pe - no stats - stub") {
+
+        options "-stub"
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                get_output_stats = false
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ]
+                input[1] = get_output_stats
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.bam).match() }
+            )
+        }
+    }
+
+    test("pe - with stats - stub") {
+
+        options "-stub"
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                get_output_stats = true
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ]
+                input[1] = get_output_stats
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.bam).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/umitools/dedup/tests/main.nf.test.snap b/modules/nf-core/umitools/dedup/tests/main.nf.test.snap
new file mode 100644
index 000000000..f7f4e94f1
--- /dev/null
+++ b/modules/nf-core/umitools/dedup/tests/main.nf.test.snap
@@ -0,0 +1,138 @@
+{
+    "pe - no stats - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T11:40:46.802233"
+    },
+    "pe - with stats - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T11:40:59.501624"
+    },
+    "pe - with stats": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.dedup.bam:md5,350e942a0d45e8356fa24bc8c47dc1ed"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.dedup_edit_distance.tsv:md5,65186b0964e2f8d970cc04d736d8b119"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.dedup_per_umi.tsv:md5,8e6783a4a79437b095f095f2aefe7c01"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.dedup_per_umi_per_position.tsv:md5,9386db4a104b8e4e32f3ca4a84efa4ac"
+                ]
+            ],
+            [
+                "versions.yml:md5,e2f5146464c09bf7ae98c85ea5410e50"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T11:27:24.231325"
+    },
+    "se - no stats - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T11:40:34.598176"
+    },
+    "se - no stats": {
+        "content": [
+            "a114abd9fccce6fe2869852b5cd18964",
+            [
+                "versions.yml:md5,e2f5146464c09bf7ae98c85ea5410e50"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T13:45:48.553561"
+    },
+    "pe - no stats": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.dedup.bam:md5,350e942a0d45e8356fa24bc8c47dc1ed"
+                ]
+            ],
+            [
+                "versions.yml:md5,e2f5146464c09bf7ae98c85ea5410e50"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T11:27:06.957467"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/umitools/dedup/tests/nextflow.config b/modules/nf-core/umitools/dedup/tests/nextflow.config
new file mode 100644
index 000000000..da6652dc3
--- /dev/null
+++ b/modules/nf-core/umitools/dedup/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: UMITOOLS_DEDUP {
+        ext.prefix = { "${meta.id}.dedup" }
+    }
+}
diff --git a/modules/nf-core/umitools/dedup/umitools-dedup.diff b/modules/nf-core/umitools/dedup/umitools-dedup.diff
deleted file mode 100644
index 327583445..000000000
--- a/modules/nf-core/umitools/dedup/umitools-dedup.diff
+++ /dev/null
@@ -1,23 +0,0 @@
-Changes in module 'nf-core/umitools/dedup'
---- modules/nf-core/umitools/dedup/main.nf
-+++ modules/nf-core/umitools/dedup/main.nf
-@@ -42,7 +42,7 @@
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
--        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
-+        umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
-     END_VERSIONS
-     """
- 
-@@ -56,7 +56,7 @@
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
--        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
-+        umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
-     END_VERSIONS
-     """
- }
-
-************************************************************
diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml
new file mode 100644
index 000000000..aab452d1e
--- /dev/null
+++ b/modules/nf-core/umitools/extract/environment.yml
@@ -0,0 +1,7 @@
+name: umitools_extract
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::umi_tools=1.1.5
diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf
index 5ffe4eb76..b97900e09 100644
--- a/modules/nf-core/umitools/extract/main.nf
+++ b/modules/nf-core/umitools/extract/main.nf
@@ -3,10 +3,10 @@ process UMITOOLS_EXTRACT {
     label "process_single"
     label "process_long"
 
-    conda "bioconda::umi_tools=1.1.4"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/umi_tools:1.1.4--py38hbff2b2d_1' :
-        'biocontainers/umi_tools:1.1.4--py38hbff2b2d_1' }"
+        'https://depot.galaxyproject.org/singularity/umi_tools:1.1.5--py39hf95cd2a_0' :
+        'biocontainers/umi_tools:1.1.5--py39hf95cd2a_0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -53,4 +53,22 @@ process UMITOOLS_EXTRACT {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.single_end) {
+        output_command = "echo '' | gzip > ${prefix}.umi_extract.fastq.gz"
+    } else {
+        output_command = "echo '' | gzip > ${prefix}.umi_extract_1.fastq.gz ;"
+        output_command += "echo '' | gzip > ${prefix}.umi_extract_2.fastq.gz"
+    }
+    """
+    touch ${prefix}.umi_extract.log
+    ${output_command}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml
index db64a0f88..7695b2717 100644
--- a/modules/nf-core/umitools/extract/meta.yml
+++ b/modules/nf-core/umitools/extract/meta.yml
@@ -1,15 +1,16 @@
 name: umitools_extract
 description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
 keywords:
-  - umitools
+  - UMI
+  - barcode
   - extract
+  - umitools
 tools:
   - umi_tools:
       description: >
-        UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
-        and single cell RNA-Seq cell barcodes
+        UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
       documentation: https://umi-tools.readthedocs.io/en/latest/
-      license: ["MIT"]
+      license: "MIT"
 input:
   - meta:
       type: map
@@ -29,9 +30,7 @@ output:
   - reads:
       type: file
       description: >
-        Extracted FASTQ files. |
-        For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
-        For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
+        Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
       pattern: "*.{fastq.gz}"
   - log:
       type: file
@@ -41,7 +40,9 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@drpatelh"
   - "@grst"
+maintainers:
+  - "@drpatelh"
+  - "@grst"
diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test b/modules/nf-core/umitools/extract/tests/main.nf.test
new file mode 100644
index 000000000..3eec566be
--- /dev/null
+++ b/modules/nf-core/umitools/extract/tests/main.nf.test
@@ -0,0 +1,102 @@
+nextflow_process {
+
+    name "Test Process UMITOOLS_EXTRACT"
+    script "../main.nf"
+    process "UMITOOLS_EXTRACT"
+    config "./nextflow.config"
+
+    test("single end") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out.reads.collect { it.collect { it instanceof Map ? it : file(it).name }},
+                    process.out.log.collect { it.collect { it instanceof Map ? it : file(it).name }},
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("single end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("pair end") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.reads[0][1][0]).name,
+                    file(process.out.reads[0][1][1]).name,
+                    process.out.log.collect { it.collect { it instanceof Map ? it : file(it).name }},
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("pair end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test.snap b/modules/nf-core/umitools/extract/tests/main.nf.test.snap
new file mode 100644
index 000000000..b1159054b
--- /dev/null
+++ b/modules/nf-core/umitools/extract/tests/main.nf.test.snap
@@ -0,0 +1,167 @@
+{
+    "pair end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,568d243174c081a0301e74ed42e59b48"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,568d243174c081a0301e74ed42e59b48"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T15:05:20.008312"
+    },
+    "single end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.umi_extract.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,568d243174c081a0301e74ed42e59b48"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.umi_extract.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,568d243174c081a0301e74ed42e59b48"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T15:04:12.145999"
+    },
+    "pair end": {
+        "content": [
+            "test.umi_extract_1.fastq.gz",
+            "test.umi_extract_2.fastq.gz",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.umi_extract.log"
+                ]
+            ],
+            [
+                "versions.yml:md5,568d243174c081a0301e74ed42e59b48"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T15:21:09.578031"
+    },
+    "single end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.umi_extract.fastq.gz"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.umi_extract.log"
+                ]
+            ],
+            [
+                "versions.yml:md5,568d243174c081a0301e74ed42e59b48"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T15:03:52.464606"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/umitools/extract/tests/nextflow.config b/modules/nf-core/umitools/extract/tests/nextflow.config
new file mode 100644
index 000000000..c866f5a00
--- /dev/null
+++ b/modules/nf-core/umitools/extract/tests/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+    withName: UMITOOLS_EXTRACT {
+        ext.args = '--bc-pattern="NNNN"'
+    }
+
+}
diff --git a/modules/nf-core/umitools/extract/umitools-extract.diff b/modules/nf-core/umitools/extract/umitools-extract.diff
deleted file mode 100644
index 464a23c00..000000000
--- a/modules/nf-core/umitools/extract/umitools-extract.diff
+++ /dev/null
@@ -1,23 +0,0 @@
-Changes in module 'nf-core/umitools/extract'
---- modules/nf-core/umitools/extract/main.nf
-+++ modules/nf-core/umitools/extract/main.nf
-@@ -33,7 +33,7 @@
- 
-         cat <<-END_VERSIONS > versions.yml
-         "${task.process}":
--            umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
-+            umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
-         END_VERSIONS
-         """
-     }  else {
-@@ -49,7 +49,7 @@
- 
-         cat <<-END_VERSIONS > versions.yml
-         "${task.process}":
--            umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
-+            umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
-         END_VERSIONS
-         """
-     }
-
-************************************************************
diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml
new file mode 100644
index 000000000..dbb1bde77
--- /dev/null
+++ b/modules/nf-core/umitools/prepareforrsem/environment.yml
@@ -0,0 +1,7 @@
+name: umitools_prepareforrsem
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::umi_tools=1.1.5
diff --git a/modules/local/umitools_prepareforrsem/main.nf b/modules/nf-core/umitools/prepareforrsem/main.nf
similarity index 54%
rename from modules/local/umitools_prepareforrsem/main.nf
rename to modules/nf-core/umitools/prepareforrsem/main.nf
index d3c2bd2c2..07c4381ad 100644
--- a/modules/local/umitools_prepareforrsem/main.nf
+++ b/modules/nf-core/umitools/prepareforrsem/main.nf
@@ -2,13 +2,13 @@ process UMITOOLS_PREPAREFORRSEM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::umi_tools=1.1.4"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/umi_tools:1.1.4--py38hbff2b2d_1' :
-        'biocontainers/umi_tools:1.1.4--py38hbff2b2d_1' }"
+        'https://depot.galaxyproject.org/singularity/umi_tools:1.1.5--py39hf95cd2a_0' :
+        'biocontainers/umi_tools:1.1.5--py39hf95cd2a_0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai)
 
     output:
     tuple val(meta), path('*.bam'), emit: bam
@@ -18,11 +18,12 @@ process UMITOOLS_PREPAREFORRSEM {
     when:
     task.ext.when == null || task.ext.when
 
-    script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
+    script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
-    prepare-for-rsem.py \\
+    umi_tools prepare-for-rsem \\
         --stdin=$bam \\
         --stdout=${prefix}.bam \\
         --log=${prefix}.prepare_for_rsem.log \\
@@ -30,7 +31,18 @@ process UMITOOLS_PREPAREFORRSEM {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        umitools: \$(umi_tools --version | sed 's/^.*UMI-tools version://; s/ *\$//')
+        umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${meta.id}.bam
+    touch ${meta.id}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/umitools/prepareforrsem/meta.yml b/modules/nf-core/umitools/prepareforrsem/meta.yml
new file mode 100644
index 000000000..8b85366cc
--- /dev/null
+++ b/modules/nf-core/umitools/prepareforrsem/meta.yml
@@ -0,0 +1,53 @@
+name: umitools_prepareforrsem
+description: Make the output from umi_tools dedup or group compatible with RSEM
+keywords:
+  - umitools
+  - rsem
+  - salmon
+  - dedup
+tools:
+  - umi_tools:
+      description: >
+        UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
+      documentation: https://umi-tools.readthedocs.io/en/latest/
+      license: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: |
+        BAM file containing reads to be deduplicated via UMIs.
+      pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: |
+        BAM index files corresponding to the input BAM file.
+      pattern: "*.{bai}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Prepared BAM file.
+      pattern: "*.{bam}"
+  - log:
+      type: file
+      description: File with logging information
+      pattern: "*.{log}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@pinin4fjords"
+maintainers:
+  - "@drpatelh"
+  - "@pinin4fjords"
diff --git a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test
new file mode 100644
index 000000000..105093505
--- /dev/null
+++ b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test
@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process UMITOOLS_PREPAREFORRSEM"
+    script "../main.nf"
+    process "UMITOOLS_PREPAREFORRSEM"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.bam).match('bam_sarscov2_bam') },
+                { assert snapshot(process.out.versions).match('versions_sarscov2_bam') }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.bam).match('bam_sarscov2_bam - stub') },
+                { assert snapshot(process.out.versions).match('versions_sarscov2_bam - stub') }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test.snap b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test.snap
new file mode 100644
index 000000000..c1e863f6f
--- /dev/null
+++ b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test.snap
@@ -0,0 +1,62 @@
+{
+    "versions_sarscov2_bam": {
+        "content": [
+            [
+                "versions.yml:md5,3403849e88fbd33fadd928f8b6ca60bb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-16T09:46:33.206750132"
+    },
+    "bam_sarscov2_bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,fe4b8302182615651e4e7784ec67c819"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-12T17:33:02.066537672"
+    },
+    "bam_sarscov2_bam - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-12T17:33:39.36279218"
+    },
+    "versions_sarscov2_bam - stub": {
+        "content": [
+            [
+                "versions.yml:md5,3403849e88fbd33fadd928f8b6ca60bb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-16T09:46:47.363697981"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml
new file mode 100644
index 000000000..4f498244a
--- /dev/null
+++ b/modules/nf-core/untar/environment.yml
@@ -0,0 +1,9 @@
+name: untar
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::grep=3.11
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index 61461c391..9bd8f5546 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -2,10 +2,10 @@ process UNTAR {
     tag "$archive"
     label 'process_single'
 
-    conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:22.04' :
+        'nf-core/ubuntu:22.04' }"
 
     input:
     tuple val(meta), path(archive)
@@ -52,8 +52,29 @@ process UNTAR {
     stub:
     prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
     """
-    mkdir $prefix
-    touch ${prefix}/file.txt
+    mkdir ${prefix}
+    ## Dry-run untaring the archive to get the files and place all in prefix
+    if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+        for i in `tar -tf ${archive}`;
+        do
+            if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]];
+            then
+                touch \${i}
+            else
+                mkdir -p \${i}
+            fi
+        done
+    else
+        for i in `tar -tf ${archive}`;
+        do
+            if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]];
+            then
+                touch ${prefix}/\${i}
+            else
+                mkdir -p ${prefix}/\${i}
+            fi
+        done
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
index db241a6e5..a9a2110f5 100644
--- a/modules/nf-core/untar/meta.yml
+++ b/modules/nf-core/untar/meta.yml
@@ -39,3 +39,8 @@ authors:
   - "@drpatelh"
   - "@matthdsm"
   - "@jfy133"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@matthdsm"
+  - "@jfy133"
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
new file mode 100644
index 000000000..f556118ff
--- /dev/null
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -0,0 +1,82 @@
+nextflow_process {
+
+    name "Test Process UNTAR"
+    script "../main.nf"
+    process "UNTAR"
+
+    test("test_untar") {
+
+        when {
+            process {
+                """
+                input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+    }
+
+    test("test_untar_onlyfiles") {
+
+        when {
+            process {
+                """
+                input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+    }
+
+    test("test_untar - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+    }
+
+    test("test_untar_onlyfiles - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap
new file mode 100644
index 000000000..ceb91b792
--- /dev/null
+++ b/modules/nf-core/untar/tests/main.nf.test.snap
@@ -0,0 +1,158 @@
+{
+    "test_untar_onlyfiles": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ],
+                "untar": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-10T12:04:28.231047"
+    },
+    "test_untar_onlyfiles - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ],
+                "untar": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-10T12:04:45.773103"
+    },
+    "test_untar - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ],
+                "untar": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-10T12:04:36.777441"
+    },
+    "test_untar": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
+                            "opts.k2d:md5,a033d00cf6759407010b21700938f543",
+                            "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ],
+                "untar": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
+                            "opts.k2d:md5,a033d00cf6759407010b21700938f543",
+                            "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-10T12:04:19.377674"
+    }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index f4d9f87e2..1771272d4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -23,7 +23,7 @@ params {
     featurecounts_group_type   = 'gene_biotype'
     gencode                    = false
     save_reference             = false
-    igenomes_base              = 's3://ngi-igenomes/igenomes'
+    igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
 
     // UMI handling
@@ -54,7 +54,7 @@ params {
     // Ribosomal RNA removal
     remove_ribo_rna            = false
     save_non_ribo_reads        = false
-    ribo_database_manifest     = "${projectDir}/assets/rrna-db-defaults.txt"
+    ribo_database_manifest     = "${projectDir}/workflows/rnaseq/assets/rrna-db-defaults.txt"
 
     // Alignment
     aligner                    = 'star_salmon'
@@ -78,6 +78,8 @@ params {
     skip_markduplicates        = false
     skip_alignment             = false
     skip_pseudo_alignment      = false
+    stranded_threshold         = 0.8
+    unstranded_threshold       = 0.1
 
     // QC
     skip_qc                    = false
@@ -102,15 +104,16 @@ params {
     multiqc_methods_description = null
 
     // Boilerplate options
-    outdir                     = null
-    publish_dir_mode           = 'copy'
-    email                      = null
-    email_on_fail              = null
-    plaintext_email            = false
-    monochrome_logs            = false
-    hook_url                   = null
-    help                       = false
-    version                    = false
+    outdir                       = null
+    publish_dir_mode             = 'copy'
+    email                        = null
+    email_on_fail                = null
+    plaintext_email              = false
+    monochrome_logs              = false
+    hook_url                     = null
+    help                         = false
+    version                      = false
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/'
 
     // Config options
     config_profile_name        = null
@@ -119,7 +122,6 @@ params {
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
-    test_data_base             = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3'
 
     // Max resource options
     // Defaults only, expecting to be overwritten
@@ -136,6 +138,15 @@ params {
 
 }
 
+// Default publishing logic for pipeline
+process {
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+}
+
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
@@ -155,97 +166,104 @@ try {
 
 profiles {
     debug {
-        dumpHashes             = true
-        process.beforeScript   = 'echo $HOSTNAME'
-        cleanup                = false
+        dumpHashes              = true
+        process.beforeScript    = 'echo $HOSTNAME'
+        cleanup                 = false
         nextflow.enable.configProcessNamesValidation = true
     }
     conda {
-        conda.enabled          = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        conda.enabled           = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        apptainer.enabled       = false
     }
     mamba {
-        conda.enabled          = true
-        conda.useMamba         = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        conda.enabled           = true
+        conda.useMamba          = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     docker {
-        docker.enabled         = true
-        conda.enabled          = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-        docker.runOptions      = '-u $(id -u):$(id -g)'
+        docker.enabled          = true
+        conda.enabled           = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+        docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
-        docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
-        singularity.enabled    = true
-        singularity.autoMounts = true
-        conda.enabled          = false
-        docker.enabled         = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+        conda.enabled           = false
+        docker.enabled          = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     podman {
-        podman.enabled         = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        podman.enabled          = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     shifter {
-        shifter.enabled        = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        shifter.enabled         = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     charliecloud {
-        charliecloud.enabled   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        apptainer.enabled      = false
+        charliecloud.enabled    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        apptainer.enabled       = false
     }
     apptainer {
-        apptainer.enabled      = true
-        apptainer.autoMounts   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+    }
+    wave {
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
     }
     gitpod {
-        executor.name          = 'local'
-        executor.cpus          = 4
-        executor.memory        = 8.GB
+        executor.name           = 'local'
+        executor.cpus           = 4
+        executor.memory         = 8.GB
     }
     test          { includeConfig 'conf/test.config'       }
-    test_cache    { includeConfig 'conf/test_cache.config' }
     test_full     { includeConfig 'conf/test_full.config'  }
     test_full_aws {
         includeConfig 'conf/test_full.config'
@@ -322,12 +340,13 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.14.0'
+    version         = '3.15.0'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+// Workflow specific config
+includeConfig "./subworkflows/local/prepare_genome/nextflow.config"
+includeConfig './workflows/rnaseq/nextflow.config'
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 42e4e8967..d89b6398e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -16,9 +16,9 @@
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
+                    "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
-                    "schema": "assets/schema_input.json",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See [usage docs](https://nf-co.re/rnaseq/usage#samplesheet-input).",
                     "fa_icon": "fas fa-file-csv"
@@ -200,7 +200,7 @@
                     "type": "string",
                     "format": "directory-path",
                     "description": "Directory / URL base for iGenomes references.",
-                    "default": "s3://ngi-igenomes/igenomes",
+                    "default": "s3://ngi-igenomes/igenomes/",
                     "fa_icon": "fas fa-cloud-download-alt",
                     "hidden": true
                 },
@@ -267,6 +267,14 @@
                     "description": "Path to directory or tar.gz archive for pre-built BBSplit index.",
                     "help_text": "The BBSplit index will have to be built at least once with this pipeline (see `--save_reference` to save index). It can then be provided via `--bbsplit_index` for future runs."
                 },
+                "sortmerna_index": {
+                    "type": "string",
+                    "format": "path",
+                    "exists": true,
+                    "fa_icon": "fas fa-bezier-curve",
+                    "description": "Path to directory or tar.gz archive for pre-built sortmerna index.",
+                    "help_text": "The sortmerna index will have to be built at least once with this pipeline (see `--save_reference` to save index). It can then be provided via `--sortmerna_index` for future runs."
+                },
                 "remove_ribo_rna": {
                     "type": "boolean",
                     "fa_icon": "fas fa-trash-alt",
@@ -278,7 +286,7 @@
                     "format": "file-path",
                     "exists": true,
                     "mimetype": "text/plain",
-                    "default": "${projectDir}/assets/rrna-db-defaults.txt",
+                    "default": "${projectDir}/workflows/rnaseq/assets/rrna-db-defaults.txt",
                     "fa_icon": "fas fa-database",
                     "description": "Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.",
                     "help_text": "By default, [rRNA databases](https://github.com/biocore/sortmerna/tree/master/data/rRNA_databases) defined in the SortMeRNA GitHub repo are used. You can see an example in the pipeline Github repository in `assets/rrna-default-dbs.txt`.\nPlease note that commercial/non-academic entities require [`licensing for SILVA`](https://www.arb-silva.de/silva-license-information) for these default databases."
@@ -444,6 +452,20 @@
                     "description": "In single-end mode, Kallisto requires an estimated standard error for fragment length. Specify a default value for that here. TODO: use existing RSeQC results to do this dynamically.",
                     "default": 200,
                     "fa_icon": "fas fa-sort-amount-up-alt"
+                },
+                "stranded_threshold": {
+                    "type": "number",
+                    "minimum": 0.5,
+                    "maximum": 1.0,
+                    "default": 0.8,
+                    "description": "The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5."
+                },
+                "unstranded_threshold": {
+                    "type": "number",
+                    "minimum": 0.0,
+                    "maximum": 1.0,
+                    "default": 0.1,
+                    "description": "The difference in fraction of stranded reads assigned to 'forward' and 'reverse' below which a sample is classified as 'unstranded'. By default the forward and reverse fractions must differ by less than 0.1 for the sample to be called as unstranded."
                 }
             }
         },
@@ -672,13 +694,6 @@
                     "description": "Institutional config URL link.",
                     "hidden": true,
                     "fa_icon": "fas fa-users-cog"
-                },
-                "test_data_base": {
-                    "type": "string",
-                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3",
-                    "description": "Base path / URL for data used in the test profiles",
-                    "help_text": "Warning: The `-profile test` samplesheet file itself contains remote paths. Setting this parameter does not alter the contents of that file.",
-                    "hidden": true
                 }
             }
         },
@@ -832,6 +847,13 @@
                     "description": "Validation of parameters in lenient more.",
                     "hidden": true,
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                },
+                "pipelines_testdata_base_path": {
+                    "type": "string",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Base URL or local path to location of pipeline test dataset files",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/",
+                    "hidden": true
                 }
             }
         }
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 000000000..0f4cac519
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,17 @@
+config {
+    // Location of nf-tests
+    testsDir "."
+
+    // nf-test directory used to create temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // Location of an optional nextflow.config file specific for executing pipeline tests
+    configFile "tests/nextflow.config"
+
+    profile "test"
+
+    // load the necessary plugins
+    plugins {
+        load "nft-bam@0.3.0"
+    }
+}
diff --git a/pyproject.toml b/pyproject.toml
deleted file mode 100644
index bc01239b3..000000000
--- a/pyproject.toml
+++ /dev/null
@@ -1,10 +0,0 @@
-# Config file for Python. Mostly used to configure linting of bin/*.py with Black.
-# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
-[tool.black]
-line-length = 120
-target_version = ["py37", "py38", "py39", "py310"]
-
-[tool.isort]
-profile = "black"
-known_first_party = ["nf_core"]
-multi_line_output = 3
diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf
index 1dba0c085..4f516e8e0 100644
--- a/subworkflows/local/align_star/main.nf
+++ b/subworkflows/local/align_star/main.nf
@@ -11,7 +11,7 @@ workflow ALIGN_STAR {
     reads               // channel: [ val(meta), [ reads ] ]
     index               // channel: [ val(meta), [ index ] ]
     gtf                 // channel: [ val(meta), [ gtf ] ]
-    star_ignore_sjdbgtf // boolean: when using pre-built STAR indices do not re-extract and use splice junctions from the GTF file 
+    star_ignore_sjdbgtf // boolean: when using pre-built STAR indices do not re-extract and use splice junctions from the GTF file
     seq_platform        // string : sequencing platform
     seq_center          // string : sequencing center
     is_aws_igenome      // boolean: whether the genome files are from AWS iGenomes
diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config
new file mode 100644
index 000000000..119eb6e4a
--- /dev/null
+++ b/subworkflows/local/align_star/nextflow.config
@@ -0,0 +1,56 @@
+if (!params.skip_alignment && params.aligner == 'star_salmon') {
+    process {
+        withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
+            ext.args   = {
+                    // Function to convert argument strings into a map
+                    def argsToMap = { String args ->
+                        args.split("\\s(?=--)").collectEntries {
+                            def parts = it.trim().split(/\s+/, 2)
+                            [(parts.first()): parts.last()]
+                        }
+                    }
+
+                    // Initialize the map with preconfigured values
+                    def preset_args_map = argsToMap("""
+                        --quantMode TranscriptomeSAM
+                        --twopassMode Basic
+                        --outSAMtype BAM Unsorted
+                        --readFilesCommand zcat
+                        --runRNGseed 0
+                        --outFilterMultimapNmax 20
+                        --alignSJDBoverhangMin 1
+                        --outSAMattributes NH HI AS NM MD
+                        --quantTranscriptomeBan Singleend
+                        --outSAMstrandField intronMotif
+                        ${params.save_unaligned ? '--outReadsUnmapped Fastx' : ''}
+                    """.trim())
+
+                    // Consolidate the extra arguments
+                    def final_args_map = preset_args_map + (params.extra_star_align_args ? argsToMap(params.extra_star_align_args) : [:])
+
+                    // Convert the map back to a list and then to a single string
+                    final_args_map.collect { key, value -> "${key} ${value}" }.join(' ').trim()
+            }
+
+            publishDir = [
+                [
+                    path: { "${params.outdir}/${params.aligner}/log" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.{out,tab}'
+                ],
+                [
+                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bam',
+                    saveAs: { params.save_align_intermeds ? it : null }
+                ],
+                [
+                    path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.fastq.gz',
+                    saveAs: { params.save_unaligned ? it : null }
+                ]
+            ]
+        }
+    }
+}
diff --git a/subworkflows/local/align_star/tests/main.nf.test b/subworkflows/local/align_star/tests/main.nf.test
new file mode 100644
index 000000000..35b3236e8
--- /dev/null
+++ b/subworkflows/local/align_star/tests/main.nf.test
@@ -0,0 +1,297 @@
+nextflow_workflow {
+
+    name "Test Subworkflow ALIGN_STAR"
+    script "../main.nf"
+    workflow "ALIGN_STAR"
+    config "./nextflow.config"
+
+    test("star - no igenomes") {
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../../modules/nf-core/star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                star_ignore_sjdbgtf = false
+                seq_platform        = 'illumina'
+                seq_center          = false
+                is_aws_igenome      = false
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = star_ignore_sjdbgtf
+                input[4] = seq_platform
+                input[5] = seq_center
+                input[6] = is_aws_igenome
+                input[7] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    file(workflow.out.log_final[0][1]).name,
+                    file(workflow.out.log_out[0][1]).name,
+                    workflow.out.bai,
+                    workflow.out.bam,
+                    workflow.out.bam_sorted,
+                    workflow.out.bam_transcript,
+                    workflow.out.csi,
+                    workflow.out.log_progress,
+                    workflow.out.fastq,
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.orig_bam,
+                    workflow.out.stats,
+                    workflow.out.tab,
+                    workflow.out.versions).match()}
+            )
+        }
+    }
+
+    test("star - with igenomes") {
+
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../../../modules/local/star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                star_ignore_sjdbgtf = false
+                seq_platform        = 'illumina'
+                seq_center          = false
+                is_aws_igenome      = true
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = star_ignore_sjdbgtf
+                input[4] = seq_platform
+                input[5] = seq_center
+                input[6] = is_aws_igenome
+                input[7] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    file(workflow.out.log_final[0][1]).name,
+                    file(workflow.out.log_out[0][1]).name,
+                    workflow.out.bai,
+                    workflow.out.bam,
+                    workflow.out.bam_sorted,
+                    workflow.out.bam_transcript,
+                    workflow.out.csi,
+                    workflow.out.log_progress,
+                    workflow.out.fastq,
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.orig_bam,
+                    workflow.out.stats,
+                    workflow.out.tab,
+                    workflow.out.versions).match()}
+            )
+        }
+    }
+
+    test("star - no igenomes - stub") {
+
+        options "-stub"
+
+        setup {
+            run("STAR_GENOMEGENERATE") {
+                script "../../../../modules/nf-core/star/genomegenerate/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test_fasta' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    ])
+                    input[1] = Channel.of([
+                        [ id:'test_gtf' ],
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                star_ignore_sjdbgtf = false
+                seq_platform        = 'illumina'
+                seq_center          = false
+                is_aws_igenome      = false
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE.out.index
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = star_ignore_sjdbgtf
+                input[4] = seq_platform
+                input[5] = seq_center
+                input[6] = is_aws_igenome
+                input[7] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.bai,
+                    workflow.out.bam,
+                    workflow.out.bam_sorted,
+                    workflow.out.bam_transcript,
+                    workflow.out.csi,
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.log_final,
+                    workflow.out.log_out,
+                    workflow.out.log_progress,
+                    workflow.out.orig_bam,
+                    workflow.out.stats,
+                    workflow.out.tab,
+                    workflow.out.versions).match()}
+            )
+        }
+    }
+
+    test("star - with igenomes - stub") {
+
+        options "-stub"
+
+        setup {
+            run("STAR_GENOMEGENERATE_IGENOMES") {
+                script "../../../../modules/local/star_genomegenerate_igenomes/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                star_ignore_sjdbgtf = false
+                seq_platform        = 'illumina'
+                seq_center          = false
+                is_aws_igenome      = true
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = STAR_GENOMEGENERATE_IGENOMES.out.index.map{ [ [id:'star'], it ] }
+                input[2] = Channel.of([
+                    [ id:'test_gtf' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+                ])
+                input[3] = star_ignore_sjdbgtf
+                input[4] = seq_platform
+                input[5] = seq_center
+                input[6] = is_aws_igenome
+                input[7] = Channel.of([
+                    [ id:'test_fasta' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.bai,
+                    workflow.out.bam,
+                    workflow.out.bam_sorted,
+                    workflow.out.bam_transcript,
+                    workflow.out.csi,
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.log_final,
+                    workflow.out.log_out,
+                    workflow.out.log_progress,
+                    workflow.out.orig_bam,
+                    workflow.out.stats,
+                    workflow.out.tab,
+                    workflow.out.versions).match()}
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/align_star/tests/main.nf.test.snap b/subworkflows/local/align_star/tests/main.nf.test.snap
new file mode 100644
index 000000000..e3a4b2e03
--- /dev/null
+++ b/subworkflows/local/align_star/tests/main.nf.test.snap
@@ -0,0 +1,498 @@
+{
+    "star - with igenomes": {
+        "content": [
+            "test.Log.final.out",
+            "test.Log.out",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam.bai:md5,8bfbd4094a92ac0de8492d98a471d1b0"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,fc154c31eb4d034ebdb6b1d17c6b45eb"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,b6cec9bba6b04b9b92eddbef128bdfbb"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Log.progress.out:md5,b2bd061d6cbaaf3d6d3b1fed547f69b8"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.flagstat:md5,db0e25cd0b37d3030e807846c022199e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.idxstats:md5,107ca94dd426cc44db316f0d402307c5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,b6cec9bba6b04b9b92eddbef128bdfbb"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.stats:md5,202e2f234f93b347b6a72d0163773054"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d"
+                ]
+            ],
+            [
+                "versions.yml:md5,06693106908e6f8f38a2c30accf7067d",
+                "versions.yml:md5,369619588c8c294b74dca9058a151b11",
+                "versions.yml:md5,78069d4515b04251f758ac52a49d9971",
+                "versions.yml:md5,b6a22ef369a375445a8f9313721b8092",
+                "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc",
+                "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T19:13:41.194686"
+    },
+    "star - no igenomes - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,06693106908e6f8f38a2c30accf7067d",
+                "versions.yml:md5,35c1cc21d26d9d8f00e6ec87e97fb634",
+                "versions.yml:md5,369619588c8c294b74dca9058a151b11",
+                "versions.yml:md5,78069d4515b04251f758ac52a49d9971",
+                "versions.yml:md5,b6a22ef369a375445a8f9313721b8092",
+                "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:43:30.675108"
+    },
+    "star - no igenomes": {
+        "content": [
+            "test.Log.final.out",
+            "test.Log.out",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam.bai:md5,8bfbd4094a92ac0de8492d98a471d1b0"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,e6573d093da6ec95f99c1669eb86bbd6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Log.progress.out:md5,b2bd061d6cbaaf3d6d3b1fed547f69b8"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.flagstat:md5,db0e25cd0b37d3030e807846c022199e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.idxstats:md5,107ca94dd426cc44db316f0d402307c5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.stats:md5,202e2f234f93b347b6a72d0163773054"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d"
+                ]
+            ],
+            [
+                "versions.yml:md5,06693106908e6f8f38a2c30accf7067d",
+                "versions.yml:md5,35c1cc21d26d9d8f00e6ec87e97fb634",
+                "versions.yml:md5,369619588c8c294b74dca9058a151b11",
+                "versions.yml:md5,78069d4515b04251f758ac52a49d9971",
+                "versions.yml:md5,b6a22ef369a375445a8f9313721b8092",
+                "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T19:12:49.496188"
+    },
+    "star - with igenomes - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,06693106908e6f8f38a2c30accf7067d",
+                "versions.yml:md5,369619588c8c294b74dca9058a151b11",
+                "versions.yml:md5,78069d4515b04251f758ac52a49d9971",
+                "versions.yml:md5,b6a22ef369a375445a8f9313721b8092",
+                "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc",
+                "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:43:56.680384"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/align_star/tests/nextflow.config b/subworkflows/local/align_star/tests/nextflow.config
new file mode 100644
index 000000000..2c26d74d6
--- /dev/null
+++ b/subworkflows/local/align_star/tests/nextflow.config
@@ -0,0 +1,12 @@
+process {
+    withName: 'STAR_GENOMEGENERATE.*' {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: 'STAR_ALIGN.*' {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded'
+    }
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 0840c7734..92f8cc04a 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -10,15 +10,18 @@ include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../../modules/nf-core/gun
 include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../../modules/nf-core/gunzip'
 
 include { UNTAR as UNTAR_BBSPLIT_INDEX      } from '../../../modules/nf-core/untar'
+include { UNTAR as UNTAR_SORTMERNA_INDEX    } from '../../../modules/nf-core/untar'
 include { UNTAR as UNTAR_STAR_INDEX         } from '../../../modules/nf-core/untar'
 include { UNTAR as UNTAR_RSEM_INDEX         } from '../../../modules/nf-core/untar'
 include { UNTAR as UNTAR_HISAT2_INDEX       } from '../../../modules/nf-core/untar'
 include { UNTAR as UNTAR_SALMON_INDEX       } from '../../../modules/nf-core/untar'
 include { UNTAR as UNTAR_KALLISTO_INDEX     } from '../../../modules/nf-core/untar'
 
+include { CUSTOM_CATADDITIONALFASTA         } from '../../../modules/nf-core/custom/catadditionalfasta'
 include { CUSTOM_GETCHROMSIZES              } from '../../../modules/nf-core/custom/getchromsizes'
 include { GFFREAD                           } from '../../../modules/nf-core/gffread'
 include { BBMAP_BBSPLIT                     } from '../../../modules/nf-core/bbmap/bbsplit'
+include { SORTMERNA as SORTMERNA_INDEX      } from '../../../modules/nf-core/sortmerna'
 include { STAR_GENOMEGENERATE               } from '../../../modules/nf-core/star/genomegenerate'
 include { HISAT2_EXTRACTSPLICESITES         } from '../../../modules/nf-core/hisat2/extractsplicesites'
 include { HISAT2_BUILD                      } from '../../../modules/nf-core/hisat2/build'
@@ -29,44 +32,48 @@ include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA       } from '../../..
 
 include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../../modules/local/preprocess_transcripts_fasta_gencode'
 include { GTF2BED                              } from '../../../modules/local/gtf2bed'
-include { CAT_ADDITIONAL_FASTA                 } from '../../../modules/local/cat_additional_fasta'
 include { GTF_FILTER                           } from '../../../modules/local/gtf_filter'
 include { STAR_GENOMEGENERATE_IGENOMES         } from '../../../modules/local/star_genomegenerate_igenomes'
 
 workflow PREPARE_GENOME {
     take:
-    fasta                //      file: /path/to/genome.fasta
-    gtf                  //      file: /path/to/genome.gtf
-    gff                  //      file: /path/to/genome.gff
-    additional_fasta     //      file: /path/to/additional.fasta
-    transcript_fasta     //      file: /path/to/transcript.fasta
-    gene_bed             //      file: /path/to/gene.bed
-    splicesites          //      file: /path/to/splicesites.txt
-    bbsplit_fasta_list   //      file: /path/to/bbsplit_fasta_list.txt
-    star_index           // directory: /path/to/star/index/
-    rsem_index           // directory: /path/to/rsem/index/
-    salmon_index         // directory: /path/to/salmon/index/
-    kallisto_index       // directory: /path/to/kallisto/index/
-    hisat2_index         // directory: /path/to/hisat2/index/
-    bbsplit_index        // directory: /path/to/rsem/index/
-    gencode              //   boolean: whether the genome is from GENCODE
-    is_aws_igenome       //   boolean: whether the genome files are from AWS iGenomes
-    biotype              //    string: if additional fasta file is provided biotype value to use when appending entries to GTF file
-    prepare_tool_indices //      list: tools to prepare indices for
-    filter_gtf           //   boolean: whether to filter GTF file
+    fasta                    //      file: /path/to/genome.fasta
+    gtf                      //      file: /path/to/genome.gtf
+    gff                      //      file: /path/to/genome.gff
+    additional_fasta         //      file: /path/to/additional.fasta
+    transcript_fasta         //      file: /path/to/transcript.fasta
+    gene_bed                 //      file: /path/to/gene.bed
+    splicesites              //      file: /path/to/splicesites.txt
+    bbsplit_fasta_list       //      file: /path/to/bbsplit_fasta_list.txt
+    sortmerna_fasta_list     //      file: /path/to/sortmerna_fasta_list.txt
+    star_index               // directory: /path/to/star/index/
+    rsem_index               // directory: /path/to/rsem/index/
+    salmon_index             // directory: /path/to/salmon/index/
+    kallisto_index           // directory: /path/to/kallisto/index/
+    hisat2_index             // directory: /path/to/hisat2/index/
+    bbsplit_index            // directory: /path/to/bbsplit/index/
+    sortmerna_index          // directory: /path/to/sortmerna/index/
+    gencode                  //   boolean: whether the genome is from GENCODE
+    featurecounts_group_type //    string: The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts
+    aligner                  //    string: Specifies the alignment algorithm to use - available options are 'star_salmon', 'star_rsem' and 'hisat2'
+    pseudo_aligner           //    string: Specifies the pseudo aligner to use - available options are 'salmon'. Runs in addition to '--aligner'
+    skip_gtf_filter          //   boolean: Skip filtering of GTF for valid scaffolds and/ or transcript IDs
+    skip_bbsplit             //   boolean: Skip BBSplit for removal of non-reference genome reads
+    skip_sortmerna           //   boolean: Skip sortmerna for removal of reads mapping to sequences in sortmerna_fasta_list
+    skip_alignment           //   boolean: Skip all of the alignment-based processes within the pipeline
+    skip_pseudo_alignment    //   boolean: Skip all of the pseudoalignment-based processes within the pipeline
 
     main:
-
     ch_versions = Channel.empty()
 
     //
     // Uncompress genome fasta file if required
     //
     if (fasta.endsWith('.gz')) {
-        ch_fasta    = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map { it[1] }
+        ch_fasta    = GUNZIP_FASTA ( [ [:], file(fasta, checkIfExists: true) ] ).gunzip.map { it[1] }
         ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions)
     } else {
-        ch_fasta = Channel.value(file(fasta))
+        ch_fasta = Channel.value(file(fasta, checkIfExists: true))
     }
 
     //
@@ -75,23 +82,41 @@ workflow PREPARE_GENOME {
     if (gtf || gff) {
         if (gtf) {
             if (gtf.endsWith('.gz')) {
-                ch_gtf      = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map { it[1] }
+                ch_gtf      = GUNZIP_GTF ( [ [:], file(gtf, checkIfExists: true) ] ).gunzip.map { it[1] }
                 ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions)
             } else {
-                ch_gtf = Channel.value(file(gtf))
+                ch_gtf = Channel.value(file(gtf, checkIfExists: true))
             }
         } else if (gff) {
             if (gff.endsWith('.gz')) {
-                ch_gff      = GUNZIP_GFF ( [ [:], gff ] ).gunzip.map { it[1] }
+                ch_gff      = GUNZIP_GFF ( [ [:], file(gff, checkIfExists: true) ] ).gunzip
                 ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions)
             } else {
-                ch_gff = Channel.value(file(gff))
+                ch_gff = Channel.value(file(gff, checkIfExists: true)).map { [ [:], it ] }
             }
-            ch_gtf      = GFFREAD ( ch_gff ).gtf
+            ch_gtf      = GFFREAD ( ch_gff, [] ).gtf.map { it[1] }
             ch_versions = ch_versions.mix(GFFREAD.out.versions)
         }
 
-    	if (filter_gtf) {
+        // Determine whether to filter the GTF or not
+        def filter_gtf =
+            ((
+                // Condition 1: Alignment is required and aligner is set
+                !skip_alignment && aligner
+            ) ||
+            (
+                // Condition 2: Pseudoalignment is required and pseudoaligner is set
+                !skip_pseudo_alignment && pseudo_aligner
+            ) ||
+            (
+                // Condition 3: Transcript FASTA file is not provided
+                !transcript_fasta
+            )) &&
+            (
+                // Condition 4: --skip_gtf_filter is not provided
+                !skip_gtf_filter
+            )
+        if (filter_gtf) {
             GTF_FILTER ( ch_fasta, ch_gtf )
             ch_gtf = GTF_FILTER.out.genome_gtf
             ch_versions = ch_versions.mix(GTF_FILTER.out.versions)
@@ -101,17 +126,23 @@ workflow PREPARE_GENOME {
     //
     // Uncompress additional fasta file and concatenate with reference fasta and gtf files
     //
+    def biotype = gencode ? "gene_type" : featurecounts_group_type
     if (additional_fasta) {
         if (additional_fasta.endsWith('.gz')) {
-            ch_add_fasta = GUNZIP_ADDITIONAL_FASTA ( [ [:], additional_fasta ] ).gunzip.map { it[1] }
+            ch_add_fasta = GUNZIP_ADDITIONAL_FASTA ( [ [:], file(additional_fasta, checkIfExists: true) ] ).gunzip.map { it[1] }
             ch_versions  = ch_versions.mix(GUNZIP_ADDITIONAL_FASTA.out.versions)
         } else {
-            ch_add_fasta = Channel.value(file(additional_fasta))
+            ch_add_fasta = Channel.value(file(additional_fasta, checkIfExists: true))
         }
-        CAT_ADDITIONAL_FASTA ( ch_fasta, ch_gtf, ch_add_fasta, biotype )
-        ch_fasta    = CAT_ADDITIONAL_FASTA.out.fasta
-        ch_gtf      = CAT_ADDITIONAL_FASTA.out.gtf
-        ch_versions = ch_versions.mix(CAT_ADDITIONAL_FASTA.out.versions)
+
+        CUSTOM_CATADDITIONALFASTA (
+            ch_fasta.combine(ch_gtf).map { fasta, gtf -> [ [:], fasta, gtf ] },
+            ch_add_fasta.map { [ [:], it ] },
+            biotype
+        )
+        ch_fasta    = CUSTOM_CATADDITIONALFASTA.out.fasta.map { it[1] }.first()
+        ch_gtf      = CUSTOM_CATADDITIONALFASTA.out.gtf.map { it[1] }.first()
+        ch_versions = ch_versions.mix(CUSTOM_CATADDITIONALFASTA.out.versions)
     }
 
     //
@@ -119,10 +150,10 @@ workflow PREPARE_GENOME {
     //
     if (gene_bed) {
         if (gene_bed.endsWith('.gz')) {
-            ch_gene_bed = GUNZIP_GENE_BED ( [ [:], gene_bed ] ).gunzip.map { it[1] }
+            ch_gene_bed = GUNZIP_GENE_BED ( [ [:], file(gene_bed, checkIfExists: true) ] ).gunzip.map { it[1] }
             ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions)
         } else {
-            ch_gene_bed = Channel.value(file(gene_bed))
+            ch_gene_bed = Channel.value(file(gene_bed, checkIfExists: true))
         }
     } else {
         ch_gene_bed = GTF2BED ( ch_gtf ).bed
@@ -134,10 +165,10 @@ workflow PREPARE_GENOME {
     //
     if (transcript_fasta) {
         if (transcript_fasta.endsWith('.gz')) {
-            ch_transcript_fasta = GUNZIP_TRANSCRIPT_FASTA ( [ [:], transcript_fasta ] ).gunzip.map { it[1] }
+            ch_transcript_fasta = GUNZIP_TRANSCRIPT_FASTA ( [ [:], file(transcript_fasta, checkIfExists: true) ] ).gunzip.map { it[1] }
             ch_versions         = ch_versions.mix(GUNZIP_TRANSCRIPT_FASTA.out.versions)
         } else {
-            ch_transcript_fasta = Channel.value(file(transcript_fasta))
+            ch_transcript_fasta = Channel.value(file(transcript_fasta, checkIfExists: true))
         }
         if (gencode) {
             PREPROCESS_TRANSCRIPTS_FASTA_GENCODE ( ch_transcript_fasta )
@@ -157,6 +188,15 @@ workflow PREPARE_GENOME {
     ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] }
     ch_versions    = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)
 
+    //
+    // Get list of indices that need to be created
+    //
+    def prepare_tool_indices = []
+    if (!skip_bbsplit) { prepare_tool_indices << 'bbsplit' }
+    if (!skip_sortmerna) { prepare_tool_indices << 'sortmerna' }
+    if (!skip_alignment) { prepare_tool_indices << aligner }
+    if (!skip_pseudo_alignment && pseudo_aligner) { prepare_tool_indices << pseudo_aligner }
+
     //
     // Uncompress BBSplit index or generate from scratch if required
     //
@@ -184,6 +224,36 @@ workflow PREPARE_GENOME {
         }
     }
 
+    //
+    // Uncompress sortmerna index or generate from scratch if required
+    //
+    ch_sortmerna_index = Channel.empty()
+    ch_rrna_fastas = Channel.empty()
+
+    if ('sortmerna' in prepare_tool_indices) {
+        ribo_db = file(sortmerna_fasta_list)
+
+        if (sortmerna_index) {
+            if (sortmerna_index.endsWith('.tar.gz')) {
+                ch_sortmerna_index = UNTAR_SORTMERNA_INDEX ( [ [:], sortmerna_index ] ).untar.map { it[1] }
+                ch_versions = ch_versions.mix(UNTAR_SORTMERNA_INDEX.out.versions)
+            } else {
+                ch_sortmerna_index = Channel.value(file(sortmerna_index))
+            }
+        } else {
+            ch_rrna_fastas = Channel.from(ribo_db.readLines())
+                .map { row -> file(row, checkIfExists: true) }
+
+            SORTMERNA_INDEX (
+                Channel.of([ [],[] ]),
+                ch_rrna_fastas.collect().map { [ 'rrna_refs', it ] },
+                Channel.of([ [],[] ])
+            )
+            ch_sortmerna_index = SORTMERNA_INDEX.out.index.first()
+            ch_versions = ch_versions.mix(SORTMERNA_INDEX.out.versions)
+        }
+    }
+
     //
     // Uncompress STAR index or generate from scratch if required
     //
@@ -197,6 +267,13 @@ workflow PREPARE_GENOME {
                 ch_star_index = Channel.value(file(star_index))
             }
         } else {
+            // Check if an AWS iGenome has been provided to use the appropriate version of STAR
+            def is_aws_igenome = false
+            if (fasta && gtf) {
+                if ((file(fasta).getName() - '.gz' == 'genome.fa') && (file(gtf).getName() - '.gz' == 'genes.gtf')) {
+                    is_aws_igenome = true
+                }
+            }
             if (is_aws_igenome) {
                 ch_star_index = STAR_GENOMEGENERATE_IGENOMES ( ch_fasta, ch_gtf ).index
                 ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE_IGENOMES.out.versions)
@@ -281,7 +358,7 @@ workflow PREPARE_GENOME {
         }
     } else {
         if ('kallisto' in prepare_tool_indices) {
-            ch_kallisto_index = KALLISTO_INDEX ( ch_transcript_fasta.map{[ [:], it]} ).index
+            ch_kallisto_index = KALLISTO_INDEX ( ch_transcript_fasta.map { [ [:], it] } ).index
             ch_versions     = ch_versions.mix(KALLISTO_INDEX.out.versions)
         }
     }
@@ -295,6 +372,8 @@ workflow PREPARE_GENOME {
     chrom_sizes      = ch_chrom_sizes            // channel: path(genome.sizes)
     splicesites      = ch_splicesites            // channel: path(genome.splicesites.txt)
     bbsplit_index    = ch_bbsplit_index          // channel: path(bbsplit/index/)
+    rrna_fastas      = ch_rrna_fastas            // channel: path(sortmerna_fasta_list)
+    sortmerna_index  = ch_sortmerna_index        // channel: path(sortmerna/index/)
     star_index       = ch_star_index             // channel: path(star/index/)
     rsem_index       = ch_rsem_index             // channel: path(rsem/index/)
     hisat2_index     = ch_hisat2_index           // channel: path(hisat2/index/)
diff --git a/subworkflows/local/prepare_genome/nextflow.config b/subworkflows/local/prepare_genome/nextflow.config
new file mode 100644
index 000000000..cb78cb9e3
--- /dev/null
+++ b/subworkflows/local/prepare_genome/nextflow.config
@@ -0,0 +1,127 @@
+process {
+    withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'UNTAR_.*' {
+        ext.args2 = '--no-same-owner'
+    }
+
+    withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'GFFREAD' {
+        ext.args   = '--keep-exon-attrs -F -T'
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'HISAT2_EXTRACTSPLICESITES' {
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'SALMON_INDEX' {
+        ext.args   = { [
+                params.gencode ? '--gencode' : '',
+                params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}": ''
+        ].join(' ').trim() }
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'KALLISTO_INDEX' {
+        ext.args   = params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}" : ''
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'RSEM_PREPAREREFERENCE_GENOME' {
+        ext.args   = '--star'
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'GTF2BED' {
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'GTF_FILTER' {
+        ext.args   = { params.skip_gtf_transcript_filter ?: '--skip_transcript_id_check' }
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'CUSTOM_GETCHROMSIZES' {
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+}
+
+if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
+    process {
+        withName: '.*:PREPARE_GENOME:BBMAP_BBSPLIT' {
+            ext.args   = 'build=1'
+            publishDir = [
+                path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+            ]
+        }
+    }
+}
+
+if (params.remove_ribo_rna && params.ribo_database_manifest) {
+    process {
+        withName: 'SORTMERNA_INDEX' {
+            ext.args   = '--index 1'
+            publishDir = [
+                path: { params.save_reference ? "${params.outdir}/genome/sortmerna" : params.outdir },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            ]
+        }
+    }
+}
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
new file mode 100644
index 000000000..fd8dc5154
--- /dev/null
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -0,0 +1,2697 @@
+nextflow_workflow {
+
+    name "Test Subworkflow PREPARE_GENOME"
+    script "../main.nf"
+    workflow "PREPARE_GENOME"
+    config "./nextflow.config"
+
+    test("default options") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gencode = false") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_gtf_filter") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = true
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_bbsplit") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = true
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_alignment") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = true
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_pseudo_alignment") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = true
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gtf = false") {
+
+        when {
+            workflow {
+                """
+                gencode                  = true
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = false
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gff = false") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = false
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gfp = false") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = false
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("transcriptome = false") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = false
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("with bed") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = file(params.pipelines_testdata_base_path + 'reference/ngscheckmate.bed', checkIfExists: true)
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("rsem_index = false") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = false
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("salmon_index = false") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = false
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("hisat2_index = false") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = false
+                input[12] = null
+                input[13] = false
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gencode = true") {
+
+        when {
+            workflow {
+                """
+                gencode                  = true
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("featurecounts_group_type = 'gene_type'") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_type'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_gtf_filter = true") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = true
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_bbsplit = true") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = true
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_alignment = true") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = true
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_pseudoalignment = true") {
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = true
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.transcript_fasta,
+                    workflow.out.salmon_index,
+                    workflow.out.fasta,
+                    workflow.out.gtf,
+                    workflow.out.fai,
+                    workflow.out.gene_bed,
+                    workflow.out.chrom_sizes,
+                    workflow.out.splicesites,
+                    workflow.out.sortmerna_index,
+                    workflow.out.star_index,
+                    workflow.out.rsem_index,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("default options - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gencode = false - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_gtf_filter - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = true
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_bbsplit - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = true
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("skip_alignment - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = true
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_pseudo_alignment - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = true
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gtf = false - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = true
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = false
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gff = false - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = false
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gfp = false - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = false
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("transcriptome = false - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = false
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("with bed - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = file(params.pipelines_testdata_base_path + 'reference/ngscheckmate.bed', checkIfExists: true)
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("rsem_index = false - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = false
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("salmon_index = false - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = false
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("hisat2_index = false - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = false
+                input[12] = null
+                input[13] = false
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("gencode = true - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = true
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("featurecounts_group_type = 'gene_type' - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_type'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_gtf_filter = true - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = true
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_bbsplit = true - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = true
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("skip_alignment = true - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = true
+                skip_pseudo_alignment    = false
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("skip_pseudoalignment = true - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                gencode                  = false
+                featurecounts_group_type = 'gene_biotype'
+                aligner                  = 'star_salmon,star_rsem,hisat2'
+                pseudo_aligner           = 'salmon,kallisto'
+                skip_gtf_filter           = false
+                skip_bbsplit             = false
+                skip_sortmerna           = true
+                skip_alignment           = false
+                skip_pseudo_alignment    = true
+
+                input[0]  = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
+                input[1]  = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
+                input[2]  = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
+                input[3]  = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
+                input[4]  = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
+                input[5]  = null
+                input[6]  = null
+                input[7]  = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
+                input[8]  = null
+                input[9]  = null
+                input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
+                input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
+                input[12] = null
+                input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
+                input[14] = null
+                input[15] = null
+                input[16] = gencode
+                input[17] = featurecounts_group_type
+                input[18] = aligner
+                input[19] = pseudo_aligner
+                input[20] = skip_gtf_filter
+                input[21] = skip_bbsplit
+                input[22] = skip_sortmerna
+                input[23] = skip_alignment
+                input[24] = skip_pseudo_alignment
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.chrom_sizes,
+                    workflow.out.fai,
+                    workflow.out.fasta,
+                    workflow.out.gene_bed,
+                    workflow.out.gtf,
+                    workflow.out.hisat2_index,
+                    workflow.out.kallisto_index,
+                    workflow.out.rsem_index,
+                    workflow.out.salmon_index,
+                    workflow.out.sortmerna_index,
+                    workflow.out.splicesites,
+                    workflow.out.star_index,
+                    workflow.out.transcript_fasta,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
new file mode 100644
index 000000000..88d78c211
--- /dev/null
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -0,0 +1,2316 @@
+{
+    "skip_gtf_filter = true - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T17:03:34.032908"
+    },
+    "skip_pseudo_alignment - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T16:59:05.328944"
+    },
+    "skip_gtf_filter": {
+        "content": [
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055"
+            ],
+            [
+                "genome_gfp.gtf:md5,5e63cda3dcafc0d6ad0a738133af9d54"
+            ],
+            [
+                "genome_gfp.fasta.fai:md5,8fa54c6bd2ea6a369efbb8ab4f30156a"
+            ],
+            [
+                "genome_gfp.bed:md5,991993ebef1def1d5823632c21177ec3"
+            ],
+            [
+                "genome_gfp.fasta.sizes:md5,9b755f8f349b14accefb4d859f84de26"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T19:15:45.003106"
+    },
+    "gencode = false - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T16:57:20.218814"
+    },
+    "gff = false - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T16:59:55.589832"
+    },
+    "skip_pseudoalignment = true - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T17:04:46.509423"
+    },
+    "featurecounts_group_type = 'gene_type' - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
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+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,2a3ed31ad34b8864fb9278dcdef596ec",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,961ab91198c4e6ec9d795b95e3f61fda",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T16:59:30.478197"
+    },
+    "gff = false": {
+        "content": [
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055"
+            ],
+            [
+                "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
+            ],
+            [
+                "genome_gfp.fasta.fai:md5,8fa54c6bd2ea6a369efbb8ab4f30156a"
+            ],
+            [
+                "genome_gfp.bed:md5,991993ebef1def1d5823632c21177ec3"
+            ],
+            [
+                "genome_gfp.fasta.sizes:md5,9b755f8f349b14accefb4d859f84de26"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T19:17:45.167724"
+    },
+    "default options - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T16:56:58.012938"
+    },
+    "salmon_index = false": {
+        "content": [
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                
+            ],
+            [
+                "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055"
+            ],
+            [
+                "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
+            ],
+            [
+                "genome_gfp.fasta.fai:md5,8fa54c6bd2ea6a369efbb8ab4f30156a"
+            ],
+            [
+                "genome_gfp.bed:md5,991993ebef1def1d5823632c21177ec3"
+            ],
+            [
+                "genome_gfp.fasta.sizes:md5,9b755f8f349b14accefb4d859f84de26"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T19:19:42.999843"
+    },
+    "rsem_index = false": {
+        "content": [
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055"
+            ],
+            [
+                "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
+            ],
+            [
+                "genome_gfp.fasta.fai:md5,8fa54c6bd2ea6a369efbb8ab4f30156a"
+            ],
+            [
+                "genome_gfp.bed:md5,991993ebef1def1d5823632c21177ec3"
+            ],
+            [
+                "genome_gfp.fasta.sizes:md5,9b755f8f349b14accefb4d859f84de26"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T19:19:19.357926"
+    },
+    "skip_alignment = true - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T17:04:20.276533"
+    },
+    "transcriptome = false - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "genome.transcripts.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,918fe0b59c0986eb602ace85841c5ab3",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T17:00:43.920677"
+    },
+    "skip_alignment = true": {
+        "content": [
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055"
+            ],
+            [
+                "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
+            ],
+            [
+                "genome_gfp.fasta.fai:md5,8fa54c6bd2ea6a369efbb8ab4f30156a"
+            ],
+            [
+                "genome_gfp.bed:md5,991993ebef1def1d5823632c21177ec3"
+            ],
+            [
+                "genome_gfp.fasta.sizes:md5,9b755f8f349b14accefb4d859f84de26"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T19:22:08.9618"
+    },
+    "skip_gtf_filter = true": {
+        "content": [
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+            ],
+            [
+                "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055"
+            ],
+            [
+                "genome_gfp.gtf:md5,5e63cda3dcafc0d6ad0a738133af9d54"
+            ],
+            [
+                "genome_gfp.fasta.fai:md5,8fa54c6bd2ea6a369efbb8ab4f30156a"
+            ],
+            [
+                "genome_gfp.bed:md5,991993ebef1def1d5823632c21177ec3"
+            ],
+            [
+                "genome_gfp.fasta.sizes:md5,9b755f8f349b14accefb4d859f84de26"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T19:21:18.583526"
+    },
+    "hisat2_index = false - stub": {
+        "content": [
+            [
+                "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+            ],
+            [
+                "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7",
+                "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T17:02:19.539518"
+    },
+    "skip_bbsplit - stub": {
+        "content": [
+            {
+                "0": [
+                    "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "10": [
+                    
+                ],
+                "11": [
+                    
+                ],
+                "12": [
+                    
+                ],
+                "13": [
+                    "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+                ],
+                "14": [
+                    
+                ],
+                "15": [
+                    "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                    "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                    "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                    "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+                ],
+                "2": [
+                    "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "3": [
+                    "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "4": [
+                    "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+                ],
+                "5": [
+                    "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    
+                ],
+                "8": [
+                    
+                ],
+                "9": [
+                    
+                ],
+                "bbsplit_index": [
+                    
+                ],
+                "chrom_sizes": [
+                    "genome_transcriptome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "fai": [
+                    "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "fasta": [
+                    "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "gene_bed": [
+                    "genome_transcriptome.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "gtf": [
+                    "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "hisat2_index": [
+                    
+                ],
+                "kallisto_index": [
+                    
+                ],
+                "rrna_fastas": [
+                    
+                ],
+                "rsem_index": [
+                    
+                ],
+                "salmon_index": [
+                    "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/salmon.tar.gz"
+                ],
+                "sortmerna_index": [
+                    
+                ],
+                "splicesites": [
+                    
+                ],
+                "star_index": [
+                    
+                ],
+                "transcript_fasta": [
+                    "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta"
+                ],
+                "versions": [
+                    "versions.yml:md5,71252f1a221be05593361acccb99506b",
+                    "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a",
+                    "versions.yml:md5,bc99889446f02427c166b3219b793672",
+                    "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T12:50:45.029123"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/prepare_genome/tests/nextflow.config b/subworkflows/local/prepare_genome/tests/nextflow.config
new file mode 100644
index 000000000..3fdd992f4
--- /dev/null
+++ b/subworkflows/local/prepare_genome/tests/nextflow.config
@@ -0,0 +1,24 @@
+process {
+    withName: 'GFFREAD' {
+        ext.args   = '--keep-exon-attrs -F -T'
+    }
+
+    withName: 'RSEM_PREPAREREFERENCE_GENOME' {
+        ext.args   = '--star'
+    }
+
+    withName: 'STAR_GENOMEGENERATE.*' {
+        ext.args = '--genomeSAindexNbases 9'
+    }
+
+    withName: 'STAR_ALIGN.*' {
+        ext.args = '--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded'
+    }
+
+    withName: 'UNTAR_.*' {
+        ext.args2 = '--no-same-owner'
+    }
+}
+
+// Fix chown issue for the output star folder
+docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)'
diff --git a/subworkflows/local/quantify_pseudo/main.nf b/subworkflows/local/quantify_pseudo/main.nf
deleted file mode 100644
index 7887f086f..000000000
--- a/subworkflows/local/quantify_pseudo/main.nf
+++ /dev/null
@@ -1,100 +0,0 @@
-//
-// Pseudoalignment and quantification with Salmon or Kallisto
-//
-
-include { SALMON_QUANT   } from '../../../modules/nf-core/salmon/quant'
-include { KALLISTO_QUANT } from '../../../modules/nf-core/kallisto/quant'
-include { TX2GENE        } from '../../../modules/local/tx2gene'
-include { TXIMPORT       } from '../../../modules/local/tximport'
-
-include { SUMMARIZEDEXPERIMENT as SE_GENE               } from '../../../modules/local/summarizedexperiment'
-include { SUMMARIZEDEXPERIMENT as SE_GENE_LENGTH_SCALED } from '../../../modules/local/summarizedexperiment'
-include { SUMMARIZEDEXPERIMENT as SE_GENE_SCALED        } from '../../../modules/local/summarizedexperiment'
-include { SUMMARIZEDEXPERIMENT as SE_TRANSCRIPT         } from '../../../modules/local/summarizedexperiment'
-
-workflow QUANTIFY_PSEUDO_ALIGNMENT {
-    take:
-    reads                     // channel: [ val(meta), [ reads ] ]
-    index                     // channel: /path/to//index/
-    transcript_fasta          // channel: /path/to/transcript.fasta
-    gtf                       // channel: /path/to/genome.gtf
-    pseudo_aligner            //     val: kallisto or salmon 
-    alignment_mode            //    bool: Run Salmon in alignment mode
-    lib_type                  //     val: String to override Salmon library type
-    kallisto_quant_fraglen    //     val: Estimated fragment length required by Kallisto in single-end mode
-    kallisto_quant_fraglen_sd //     val: Estimated standard error for fragment length required by Kallisto in single-end mode 
-
-    main:
-
-    ch_versions = Channel.empty()
-
-    //
-    // Quantify and merge counts across samples
-    //
-    // NOTE: MultiQC needs Salmon outputs, but Kallisto logs
-    if (pseudo_aligner == 'salmon') {
-        SALMON_QUANT ( reads, index, gtf, transcript_fasta, alignment_mode, lib_type )
-        ch_pseudo_results = SALMON_QUANT.out.results
-        ch_pseudo_multiqc = ch_pseudo_results
-        ch_versions = ch_versions.mix(SALMON_QUANT.out.versions.first())
-    } else {
-        KALLISTO_QUANT ( reads, index, gtf, [], kallisto_quant_fraglen, kallisto_quant_fraglen_sd)
-        ch_pseudo_results = KALLISTO_QUANT.out.results
-        ch_pseudo_multiqc = KALLISTO_QUANT.out.log
-        ch_versions = ch_versions.mix(KALLISTO_QUANT.out.versions.first())
-    }
-
-    TX2GENE ( ch_pseudo_results.collect{it[1]}, pseudo_aligner, gtf )
-    ch_versions = ch_versions.mix(TX2GENE.out.versions)
-
-    TXIMPORT ( ch_pseudo_results.collect{it[1]}, TX2GENE.out.tsv.collect(), pseudo_aligner )
-    ch_versions = ch_versions.mix(TXIMPORT.out.versions)
-
-    SE_GENE (
-        TXIMPORT.out.counts_gene,
-        TXIMPORT.out.tpm_gene,
-        TX2GENE.out.tsv.collect()
-    )
-    ch_versions = ch_versions.mix(SE_GENE.out.versions)
-
-    SE_GENE_LENGTH_SCALED (
-        TXIMPORT.out.counts_gene_length_scaled,
-        TXIMPORT.out.tpm_gene,
-        TX2GENE.out.tsv.collect()
-    )
-
-    SE_GENE_SCALED (
-        TXIMPORT.out.counts_gene_scaled,
-        TXIMPORT.out.tpm_gene,
-        TX2GENE.out.tsv.collect()
-    )
-
-    SE_TRANSCRIPT (
-        TXIMPORT.out.counts_transcript,
-        TXIMPORT.out.tpm_transcript,
-        TX2GENE.out.tsv.collect()
-    )
-
-    emit:
-    results                       = ch_pseudo_results                      // channel: [ val(meta), results_dir ]
-    multiqc                       = ch_pseudo_multiqc                      // channel: [ val(meta), files_for_multiqc ]
-
-    tpm_gene                      = TXIMPORT.out.tpm_gene                  //    path *gene_tpm.tsv
-    counts_gene                   = TXIMPORT.out.counts_gene               //    path *gene_counts.tsv
-    lengths_gene                  = TXIMPORT.out.lengths_gene              //    path *gene_lengths.tsv
-    counts_gene_length_scaled     = TXIMPORT.out.counts_gene_length_scaled //    path *gene_counts_length_scaled.tsv
-    counts_gene_scaled            = TXIMPORT.out.counts_gene_scaled        //    path *gene_counts_scaled.tsv
-    tpm_transcript                = TXIMPORT.out.tpm_transcript            //    path *gene_tpm.tsv
-    counts_transcript             = TXIMPORT.out.counts_transcript         //    path *transcript_counts.tsv
-    lengths_transcript            = TXIMPORT.out.lengths_transcript        //    path *transcript_lengths.tsv
-
-    merged_gene_rds               = SE_GENE.out.rds                        //    path: *.rds
-    merged_gene_rds_length_scaled = SE_GENE_LENGTH_SCALED.out.rds          //    path: *.rds
-    merged_gene_rds_scaled        = SE_GENE_SCALED.out.rds                 //    path: *.rds
-
-    merged_counts_transcript      = TXIMPORT.out.counts_transcript         //    path: *.transcript_counts.tsv
-    merged_tpm_transcript         = TXIMPORT.out.tpm_transcript            //    path: *.transcript_tpm.tsv
-    merged_transcript_rds         = SE_TRANSCRIPT.out.rds                  //    path: *.rds
-
-    versions                      = ch_versions                            // channel: [ versions.yml ]
-}
diff --git a/subworkflows/local/quantify_rsem/nextflow.config b/subworkflows/local/quantify_rsem/nextflow.config
new file mode 100644
index 000000000..7b50b86c0
--- /dev/null
+++ b/subworkflows/local/quantify_rsem/nextflow.config
@@ -0,0 +1,39 @@
+if (!params.skip_alignment && params.aligner == 'star_rsem') {
+    process {
+        withName: '.*:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION' {
+            ext.args   = [
+                '--star',
+                '--star-output-genome-bam',
+                '--star-gzipped-read-file',
+                '--estimate-rspd',
+                '--seed 1'
+            ].join(' ').trim()
+            publishDir = [
+                [
+                    path: { "${params.outdir}/${params.aligner}" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.{stat,results}"
+                ],
+                [
+                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.bam",
+                    saveAs: { params.save_align_intermeds ? it : null }
+                ],
+                [
+                    path: { "${params.outdir}/${params.aligner}/log" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.log"
+                ]
+            ]
+        }
+
+        withName: '.*:QUANTIFY_RSEM:RSEM_MERGE_COUNTS' {
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+    }
+}
diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test b/subworkflows/local/quantify_rsem/tests/main.nf.test
new file mode 100644
index 000000000..bba6f4372
--- /dev/null
+++ b/subworkflows/local/quantify_rsem/tests/main.nf.test
@@ -0,0 +1,105 @@
+nextflow_workflow {
+
+    name "Test Workflow QUANTIFY_RSEM"
+    script "../main.nf"
+    workflow "QUANTIFY_RSEM"
+    config "./nextflow.config"
+
+    test("homo_sapiens") {
+
+        setup {
+            run("RSEM_PREPAREREFERENCE") {
+                script "../../../../modules/nf-core/rsem/preparereference/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                    input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true))
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', strandedness: 'forward' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = RSEM_PREPAREREFERENCE.out.index
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    file(workflow.out.logs[0][1]).name,
+                    workflow.out.counts_gene,
+                    workflow.out.counts_transcript,
+                    workflow.out.stat,
+                    workflow.out.bam_star,
+                    workflow.out.bam_genome,
+                    workflow.out.bam_transcript,
+                    workflow.out.counts_transcript,
+                    workflow.out.bam,
+                    workflow.out.bai,
+                    workflow.out.csi,
+                    workflow.out.stats,
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.merged_counts_gene,
+                    workflow.out.merged_tpm_gene,
+                    workflow.out.merged_counts_transcript,
+                    workflow.out.merged_tpm_transcript,
+                    workflow.out.versions
+                ).match()}
+            )
+        }
+    }
+
+    test("homo_sapiens - stub") {
+
+        options "-stub"
+
+        setup {
+            run("RSEM_PREPAREREFERENCE") {
+                script "../../../../modules/nf-core/rsem/preparereference/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
+                    input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true))
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', strandedness: 'forward' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = RSEM_PREPAREREFERENCE.out.index
+                input[2] = Channel.of([[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test.snap b/subworkflows/local/quantify_rsem/tests/main.nf.test.snap
new file mode 100644
index 000000000..847be5d62
--- /dev/null
+++ b/subworkflows/local/quantify_rsem/tests/main.nf.test.snap
@@ -0,0 +1,376 @@
+{
+    "homo_sapiens - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "13": [
+                    "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "14": [
+                    "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "15": [
+                    "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "16": [
+                    "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "17": [
+                    "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9",
+                    "versions.yml:md5,3399809728955f4654ab781f37ea42d3",
+                    "versions.yml:md5,4219f710ca21b71a7c7db6b02ac19bb3",
+                    "versions.yml:md5,912c613bca84f899b3e890985ecc6fc2",
+                    "versions.yml:md5,a4755dd9acbfa60dbc38e172ffda193f",
+                    "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c",
+                    "versions.yml:md5,f645ee5b20a4e89c6ed48fdc27c21791"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_genome": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_star": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_transcript": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_gene": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_transcript": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "logs": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_counts_gene": [
+                    "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "merged_counts_transcript": [
+                    "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "merged_tpm_gene": [
+                    "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "merged_tpm_transcript": [
+                    "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "stat": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9",
+                    "versions.yml:md5,3399809728955f4654ab781f37ea42d3",
+                    "versions.yml:md5,4219f710ca21b71a7c7db6b02ac19bb3",
+                    "versions.yml:md5,912c613bca84f899b3e890985ecc6fc2",
+                    "versions.yml:md5,a4755dd9acbfa60dbc38e172ffda193f",
+                    "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c",
+                    "versions.yml:md5,f645ee5b20a4e89c6ed48fdc27c21791"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:32:06.579549"
+    },
+    "homo_sapiens": {
+        "content": [
+            "test.log",
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.genes.results:md5,c7ec226f76736ea805771e73553ae359"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    [
+                        "test.cnt:md5,76249e6b2f3c104f414aae596ba2c2f4",
+                        "test.model:md5,a7a4bc1734918ef5848604e3362b83e2",
+                        "test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.transcript.bam:md5,ed681d39f5700ffc74d6321525330d93"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "strandedness": "forward"
+                    },
+                    "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "rsem.merged.gene_counts.tsv:md5,f3b586000c97c89aec45360772e73df1"
+            ],
+            [
+                "rsem.merged.gene_tpm.tsv:md5,e6ae3dfa9913a7c15b705ec27c376212"
+            ],
+            [
+                "rsem.merged.transcript_counts.tsv:md5,235c002b811360183494a2aac74d1f5b"
+            ],
+            [
+                "rsem.merged.transcript_tpm.tsv:md5,d38f22667e3b8012f1d783b8d5159ccc"
+            ],
+            [
+                "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9",
+                "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T19:53:14.561568"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/quantify_rsem/tests/nextflow.config b/subworkflows/local/quantify_rsem/tests/nextflow.config
new file mode 100644
index 000000000..51fecdb1f
--- /dev/null
+++ b/subworkflows/local/quantify_rsem/tests/nextflow.config
@@ -0,0 +1,12 @@
+process {
+
+    // Needs the glob to force the config to be applied
+    withName: "RSEM_PREPAREREFERENCE" {
+        ext.args = "--star "
+    }
+
+    withName: "RSEM_CALCULATEEXPRESSION" {
+        ext.args = '--star --star-gzipped-read-file'
+    }
+
+}
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
new file mode 100644
index 000000000..b2b890479
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
@@ -0,0 +1,600 @@
+//
+// Subworkflow with functionality specific to the nf-core/rnaseq pipeline
+//
+
+import groovy.json.JsonSlurper
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-validation'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
+include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
+include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { logColours                } from '../../nf-core/utils_nfcore_pipeline'
+include { calculateStrandedness     } from '../../nf-core/fastq_qc_trim_filter_setstrandedness'
+
+/*
+========================================================================================
+    SUBWORKFLOW TO INITIALISE PIPELINE
+========================================================================================
+*/
+
+workflow PIPELINE_INITIALISATION {
+
+    take:
+    version           // boolean: Display version and exit
+    help              // boolean: Display help text
+    schema            //  string: Path to the JSON schema file
+    validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
+    monochrome_logs   // boolean: Do not use coloured log outputs
+    nextflow_cli_args  //   array: List of positional nextflow CLI args
+    outdir            //  string: The output directory where the results will be saved
+
+    main:
+
+    //
+    // Print version and exit if required and dump pipeline parameters to JSON file
+    //
+    UTILS_NEXTFLOW_PIPELINE (
+        version,
+        true,
+        outdir,
+        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
+    )
+
+    //
+    // Validate parameters and generate parameter summary to stdout
+    //
+    pre_help_text = nfCoreLogo(monochrome_logs)
+    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
+    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --genome GRCh37 --outdir <OUTDIR>"
+    UTILS_NFVALIDATION_PLUGIN (
+        help,
+        workflow_command,
+        pre_help_text,
+        post_help_text,
+        validate_params,
+        schema
+    )
+
+    //
+    // Check config provided to the pipeline
+    //
+    UTILS_NFCORE_PIPELINE (
+        nextflow_cli_args
+    )
+
+    //
+    // Custom validation for pipeline parameters
+    //
+    validateInputParameters()
+
+}
+
+/*
+========================================================================================
+    SUBWORKFLOW FOR PIPELINE COMPLETION
+========================================================================================
+*/
+
+def pass_mapped_reads  = [:]
+def pass_trimmed_reads = [:]
+def pass_strand_check  = [:]
+
+workflow PIPELINE_COMPLETION {
+
+    take:
+    schema             //  string: Path to the JSON schema file
+    email              //  string: email address
+    email_on_fail      //  string: email address sent on pipeline failure
+    plaintext_email    // boolean: Send plain-text email instead of HTML
+    outdir             //    path: Path to output directory where results will be published
+    monochrome_logs    // boolean: Disable ANSI colour codes in log output
+    hook_url           //  string: hook URL for notifications
+    multiqc_report     //  string: Path to MultiQC report
+    trim_status        // map: pass/fail status per sample for trimming
+    map_status         // map: pass/fail status per sample for mapping
+    strand_status      // map: pass/fail status per sample for strandedness check
+
+    main:
+
+    summary_params = paramsSummaryMap(workflow, parameters_schema: schema)
+
+    trim_status
+        .map{
+            id, status -> pass_trimmed_reads[id] = status
+        }
+
+    map_status
+        .map{
+            id, status -> pass_mapped_reads[id] = status
+        }
+
+    strand_status
+        .map{
+            id, status -> pass_strand_check[id] = status
+        }
+
+    //
+    // Completion email and summary
+    //
+    workflow.onComplete {
+        if (email || email_on_fail) {
+            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+        }
+
+        rnaseqSummary(monochrome_logs=monochrome_logs, pass_mapped_reads=pass_mapped_reads, pass_trimmed_reads=pass_trimmed_reads, pass_strand_check=pass_strand_check)
+
+        if (hook_url) {
+            imNotification(summary_params, hook_url)
+        }
+    }
+
+    workflow.onError {
+        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+    }
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+// Function to check samples are internally consistent after being grouped
+//
+def checkSamplesAfterGrouping(input) {
+    def (metas, fastqs) = input[1..2]
+
+    // Check that multiple runs of the same sample are of the same strandedness
+    def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1
+    if (!strandedness_ok) {
+        error("Please check input samplesheet -> Multiple runs of a sample must have the same strandedness!: ${metas[0].id}")
+    }
+
+    // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
+    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
+    if (!endedness_ok) {
+        error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
+    }
+
+    return [ metas[0], fastqs ]
+}
+
+//
+// Check and validate pipeline parameters
+//
+def validateInputParameters() {
+
+    genomeExistsError()
+
+    if (!params.fasta) {
+        error("Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.")
+    }
+
+    if (!params.gtf && !params.gff) {
+        error("No GTF or GFF3 annotation specified! The pipeline requires at least one of these files.")
+    }
+
+    if (params.gtf) {
+        if (params.gff) {
+            gtfGffWarn()
+        }
+        if (params.genome == 'GRCh38' && params.gtf.contains('Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf')) {
+            ncbiGenomeWarn()
+        }
+        if (params.gtf.contains('/UCSC/') && params.gtf.contains('Annotation/Genes/genes.gtf')) {
+            ucscGenomeWarn()
+        }
+    }
+
+    if (params.transcript_fasta) {
+        transcriptsFastaWarn()
+    }
+
+    if (!params.skip_bbsplit && !params.bbsplit_index && !params.bbsplit_fasta_list) {
+        error("Please provide either --bbsplit_fasta_list / --bbsplit_index to run BBSplit.")
+    }
+
+    if (params.remove_ribo_rna && !params.ribo_database_manifest) {
+        error("Please provide --ribo_database_manifest to remove ribosomal RNA with SortMeRNA.")
+    }
+
+    if (params.with_umi && !params.skip_umi_extract) {
+        if (!params.umitools_bc_pattern && !params.umitools_bc_pattern2) {
+            error("UMI-tools requires a barcode pattern to extract barcodes from the reads.")
+        }
+    }
+
+    if (params.skip_alignment) {
+        skipAlignmentWarn()
+    }
+
+    if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
+        if (!(params.salmon_index || params.transcript_fasta || (params.fasta && (params.gtf || params.gff)))) {
+            error("To use `--pseudo_aligner 'salmon'`, you must provide either --salmon_index or --transcript_fasta or both --fasta and --gtf / --gff.")
+        }
+    }
+
+    // Checks when running --aligner star_rsem
+    if (!params.skip_alignment && params.aligner == 'star_rsem') {
+        if (params.with_umi) {
+            rsemUmiError()
+        }
+        if (params.rsem_index && params.star_index) {
+            rsemStarIndexWarn()
+        }
+        if (params.aligner  == 'star_rsem' && params.extra_star_align_args) {
+            rsemStarExtraArgumentsWarn()
+        }
+    }
+
+    // Warn if --additional_fasta provided with aligner index
+    if (!params.skip_alignment && params.additional_fasta) {
+        def index = ''
+        if (params.aligner == 'star_salmon' && params.star_index) {
+            index = 'star'
+        }
+        if (params.aligner == 'star_rsem' && params.rsem_index) {
+            index = 'rsem'
+        }
+        if (params.aligner == 'hisat2' && params.hisat2_index) {
+            index = 'hisat2'
+        }
+        if (index) {
+            additionaFastaIndexWarn(index)
+        }
+    }
+
+    // Check which RSeQC modules we are running
+    def valid_rseqc_modules = ['bam_stat', 'inner_distance', 'infer_experiment', 'junction_annotation', 'junction_saturation', 'read_distribution', 'read_duplication', 'tin']
+    def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
+    if ((valid_rseqc_modules + rseqc_modules).unique().size() != valid_rseqc_modules.size()) {
+        error("Invalid option: ${params.rseqc_modules}. Valid options for '--rseqc_modules': ${valid_rseqc_modules.join(', ')}")
+    }
+
+    // Check rRNA databases for sortmerna
+    if (params.remove_ribo_rna) {
+        ch_ribo_db = file(params.ribo_database_manifest)
+        if (ch_ribo_db.isEmpty()) {
+            error("File provided with --ribo_database_manifest is empty: ${ch_ribo_db.getName()}!")
+        }
+    }
+
+    // Check if file with list of fastas is provided when running BBSplit
+    if (!params.skip_bbsplit && !params.bbsplit_index && params.bbsplit_fasta_list) {
+        ch_bbsplit_fasta_list = file(params.bbsplit_fasta_list)
+        if (ch_bbsplit_fasta_list.isEmpty()) {
+            error("File provided with --bbsplit_fasta_list is empty: ${ch_bbsplit_fasta_list.getName()}!")
+        }
+    }
+}
+
+//
+// Exit pipeline if incorrect --genome key provided
+//
+def genomeExistsError() {
+    if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
+            "  Currently, the available genome keys are:\n" +
+            "  ${params.genomes.keySet().join(", ")}\n" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        error(error_string)
+    }
+}
+
+//
+// Generate methods description for MultiQC
+//
+def toolCitationText() {
+    // TODO nf-core: Optionally add in-text citation tools to this list.
+    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
+    // Uncomment function in methodsDescriptionText to render in MultiQC report
+    def citation_text = [
+            "Tools used in the workflow included:",
+            "FastQC (Andrews 2010),",
+            "MultiQC (Ewels et al. 2016)",
+            "."
+        ].join(' ').trim()
+
+    return citation_text
+}
+
+def toolBibliographyText() {
+    // TODO nf-core: Optionally add bibliographic entries to this list.
+    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
+    // Uncomment function in methodsDescriptionText to render in MultiQC report
+    def reference_text = [
+            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
+            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
+        ].join(' ').trim()
+
+    return reference_text
+}
+
+def methodsDescriptionText(mqc_methods_yaml) {
+    // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+    def meta = [:]
+    meta.workflow = workflow.toMap()
+    meta["manifest_map"] = workflow.manifest.toMap()
+
+    // Pipeline DOI
+    if (meta.manifest_map.doi) {
+        // Using a loop to handle multiple DOIs
+        // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+        // Removing ` ` since the manifest.doi is a string and not a proper list
+        def temp_doi_ref = ""
+        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
+        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
+    } else meta["doi_text"] = ""
+    meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+
+    // Tool references
+    meta["tool_citations"] = ""
+    meta["tool_bibliography"] = ""
+
+    // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
+    // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    // meta["tool_bibliography"] = toolBibliographyText()
+    def methods_text = mqc_methods_yaml.text
+
+    def engine =  new groovy.text.SimpleTemplateEngine()
+    def description_html = engine.createTemplate(methods_text).make(meta)
+
+    return description_html.toString()
+}
+
+//
+// Print a warning if both GTF and GFF have been provided
+//
+def gtfGffWarn() {
+    log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        "  Both '--gtf' and '--gff' parameters have been provided.\n" +
+        "  Using GTF file as priority.\n" +
+        "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+}
+
+//
+// Print a warning if using GRCh38 assembly from igenomes.config
+//
+def ncbiGenomeWarn() {
+    log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        "  When using '--genome GRCh38' the assembly is from the NCBI and NOT Ensembl.\n" +
+        "  Biotype QC will be skipped to circumvent the issue below:\n" +
+        "  https://github.com/nf-core/rnaseq/issues/460\n\n" +
+        "  If you would like to use the soft-masked Ensembl assembly instead please see:\n" +
+        "  https://github.com/nf-core/rnaseq/issues/159#issuecomment-501184312\n" +
+        "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+}
+
+//
+// Print a warning if using a UCSC assembly from igenomes.config
+//
+def ucscGenomeWarn() {
+    log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        "  When using UCSC assemblies the 'gene_biotype' field is absent from the GTF file.\n" +
+        "  Biotype QC will be skipped to circumvent the issue below:\n" +
+        "  https://github.com/nf-core/rnaseq/issues/460\n\n" +
+        "  If you would like to use the soft-masked Ensembl assembly instead please see:\n" +
+        "  https://github.com/nf-core/rnaseq/issues/159#issuecomment-501184312\n" +
+        "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+}
+
+//
+// Print a warning if using '--transcript_fasta'
+//
+def transcriptsFastaWarn() {
+    log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        "  '--transcript_fasta' parameter has been provided.\n" +
+        "  Make sure transcript names in this file match those in the GFF/GTF file.\n\n" +
+        "  Please see:\n" +
+        "  https://github.com/nf-core/rnaseq/issues/753\n" +
+        "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+}
+
+//
+// Print a warning if --skip_alignment has been provided
+//
+def skipAlignmentWarn() {
+    log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        "  '--skip_alignment' parameter has been provided.\n" +
+        "  Skipping alignment, genome-based quantification and all downstream QC processes.\n" +
+        "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+}
+
+//
+// Print a warning if using '--aligner star_rsem' and '--with_umi'
+//
+def rsemUmiError() {
+    def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        "  When using '--aligner star_rsem', STAR is run by RSEM itself and so it is\n" +
+        "  not possible to remove UMIs before the quantification.\n\n" +
+        "  If you would like to remove UMI barcodes using the '--with_umi' option\n" +
+        "  please use either '--aligner star_salmon' or '--aligner hisat2'.\n" +
+        "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+    error(error_string)
+}
+
+//
+// Print a warning if using '--aligner star_rsem' and providing both '--rsem_index' and '--star_index'
+//
+def rsemStarIndexWarn() {
+    log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        "  When using '--aligner star_rsem', both the STAR and RSEM indices should\n" +
+        "  be present in the path specified by '--rsem_index'.\n\n" +
+        "  This warning has been generated because you have provided both\n" +
+        "  '--rsem_index' and '--star_index'. The pipeline will ignore the latter.\n\n" +
+        "  Please see:\n" +
+        "  https://github.com/nf-core/rnaseq/issues/568\n" +
+        "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+}
+
+//
+// Print a warning if using '--aligner star_rsem' and providing '--star_extra_alignment_args'
+//
+def rsemStarExtraArgumentsWarn() {
+    log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        "  No additional arguments can be passed to STAR when using RSEM.\n" +
+        "  Because RSEM enforces its own parameters for STAR, any extra arguments\n" +
+        "  to STAR will be ignored. Alternatively, choose the STAR+Salmon route.\n\n" +
+        "  This warning has been generated because you have provided both\n" +
+        "  '--aligner star_rsem' and '--extra_star_align_args'.\n\n" +
+        "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+}
+
+//
+// Print a warning if using '--additional_fasta' and '--<ALIGNER>_index'
+//
+def additionaFastaIndexWarn(index) {
+    log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        "  When using '--additional_fasta <FASTA_FILE>' the aligner index will not\n" +
+        "  be re-built with the transgenes incorporated by default since you have \n" +
+        "  already provided an index via '--${index}_index <INDEX>'.\n\n" +
+        "  Set '--additional_fasta <FASTA_FILE> --${index}_index false --gene_bed false --save_reference'\n" +
+        "  to re-build the index with transgenes included and the index and gene BED file will be saved in\n" +
+        "  'results/genome/index/${index}/' for re-use with '--${index}_index'.\n\n" +
+        "  Ignore this warning if you know that the index already contains transgenes.\n\n" +
+        "  Please see:\n" +
+        "  https://github.com/nf-core/rnaseq/issues/556\n" +
+        "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+}
+
+//
+// Function to generate an error if contigs in genome fasta file > 512 Mbp
+//
+def checkMaxContigSize(fai_file) {
+    def max_size = 512000000
+    fai_file.eachLine { line ->
+        def lspl  = line.split('\t')
+        def chrom = lspl[0]
+        def size  = lspl[1]
+        if (size.toInteger() > max_size) {
+            def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+                "  Contig longer than ${max_size}bp found in reference genome!\n\n" +
+                "  ${chrom}: ${size}\n\n" +
+                "  Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.\n\n" +
+                "  Please see:\n" +
+                "  https://github.com/nf-core/rnaseq/issues/744\n" +
+                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+            error(error_string)
+        }
+    }
+}
+
+//
+// Function that parses and returns the alignment rate from the STAR log output
+//
+def getStarPercentMapped(params, align_log) {
+    def percent_aligned = 0
+    def pattern = /Uniquely mapped reads %\s*\|\s*([\d\.]+)%/
+    align_log.eachLine { line ->
+        def matcher = line =~ pattern
+        if (matcher) {
+            percent_aligned = matcher[0][1].toFloat()
+        }
+    }
+
+    def pass = false
+    if (percent_aligned >= params.min_mapped_reads.toFloat()) {
+        pass = true
+    }
+    return [ percent_aligned, pass ]
+}
+
+//
+// Function to check whether biotype field exists in GTF file
+//
+def biotypeInGtf(gtf_file, biotype) {
+    def hits = 0
+    gtf_file.eachLine { line ->
+        def attributes = line.split('\t')[-1].split()
+        if (attributes.contains(biotype)) {
+            hits += 1
+        }
+    }
+    if (hits) {
+        return true
+    } else {
+        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            "  Biotype attribute '${biotype}' not found in the last column of the GTF file!\n\n" +
+            "  Biotype QC will be skipped to circumvent the issue below:\n" +
+            "  https://github.com/nf-core/rnaseq/issues/460\n\n" +
+            "  Amend '--featurecounts_group_type' to change this behaviour.\n" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        return false
+    }
+}
+
+//
+// Function that parses RSeQC infer_experiment output file to get inferred strandedness
+//
+def getInferexperimentStrandedness(inferexperiment_file, stranded_threshold = 0.8, unstranded_threshold = 0.1) {
+    def forwardFragments = 0
+    def reverseFragments = 0
+    def unstrandedFragments = 0
+
+    inferexperiment_file.eachLine { line ->
+        def unstranded_matcher = line =~ /Fraction of reads failed to determine:\s([\d\.]+)/
+        def se_sense_matcher = line =~ /Fraction of reads explained by "\++,--":\s([\d\.]+)/
+        def se_antisense_matcher = line =~ /Fraction of reads explained by "\+-,-\+":\s([\d\.]+)/
+        def pe_sense_matcher = line =~ /Fraction of reads explained by "1\++,1--,2\+-,2-\+":\s([\d\.]+)/
+        def pe_antisense_matcher = line =~ /Fraction of reads explained by "1\+-,1-\+,2\+\+,2--":\s([\d\.]+)/
+
+        if (unstranded_matcher) unstrandedFragments = unstranded_matcher[0][1].toFloat() * 100
+        if (se_sense_matcher) forwardFragments = se_sense_matcher[0][1].toFloat() * 100
+        if (se_antisense_matcher) reverseFragments = se_antisense_matcher[0][1].toFloat() * 100
+        if (pe_sense_matcher) forwardFragments = pe_sense_matcher[0][1].toFloat() * 100
+        if (pe_antisense_matcher) reverseFragments = pe_antisense_matcher[0][1].toFloat() * 100
+    }
+
+    // Use shared calculation function to determine strandedness
+    return calculateStrandedness(forwardFragments, reverseFragments, unstrandedFragments, stranded_threshold, unstranded_threshold)
+}
+
+//
+// Print pipeline summary on completion
+//
+def rnaseqSummary(monochrome_logs=true, pass_mapped_reads=[:], pass_trimmed_reads=[:], pass_strand_check=[:]) {
+    def colors = logColours(monochrome_logs)
+
+    def fail_mapped_count  = pass_mapped_reads.count  { key, value -> value == false }
+    def fail_trimmed_count = pass_trimmed_reads.count { key, value -> value == false }
+    def fail_strand_count  = pass_strand_check.count  { key, value -> value == false }
+    if (workflow.success) {
+        def color = colors.green
+        def status = []
+        if (workflow.stats.ignoredCount != 0) {
+            color = colors.yellow
+            status += ['with errored process(es)']
+        }
+        if (fail_mapped_count > 0 || fail_trimmed_count > 0) {
+            color = colors.yellow
+            status += ['with skipped sampl(es)']
+        }
+        log.info "-${colors.purple}[$workflow.manifest.name]${color} Pipeline completed successfully ${status.join(', ')}${colors.reset}-"
+        if (fail_trimmed_count > 0) {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_trimmed_count}/${pass_trimmed_reads.size()} samples skipped since they failed ${params.min_trimmed_reads} trimmed read threshold.${colors.reset}-"
+        }
+        if (fail_mapped_count > 0) {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_mapped_count}/${pass_mapped_reads.size()} samples skipped since they failed STAR ${params.min_mapped_reads}% mapped threshold.${colors.reset}-"
+        }
+        if (fail_strand_count > 0) {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_strand_count}/${pass_strand_check.size()} samples failed strandedness check.${colors.reset}-"
+        }
+    } else {
+        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+    }
+}
+
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test
new file mode 100644
index 000000000..b394aadb7
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test
@@ -0,0 +1,501 @@
+nextflow_function {
+
+    name "Test Functions"
+    script "../main.nf"
+
+    test("Test Function checkSamplesAfterGrouping success") {
+
+        function "checkSamplesAfterGrouping"
+
+        when {
+            function {
+                """
+                input[0] = [
+                    [],
+                    [
+                        [ id: 'test', strandedness: 'unstranded', single_end: true ],
+                        [ id: 'test', strandedness: 'unstranded', single_end: true ]
+                    ],
+                    [
+                        [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ],
+                        [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function checkSamplesAfterGrouping invalid strandedness") {
+
+        function "checkSamplesAfterGrouping"
+
+        when {
+            function {
+                """
+                input[0] = [
+                    [],
+                    [
+                        [ id: 'test', strandedness: 'unstranded', single_end: true ],
+                        [ id: 'test', strandedness: 'stranded', single_end: true ]
+                    ],
+                    [
+                        [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ],
+                        [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.failed },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function checkSamplesAfterGrouping invalid endedness") {
+
+        function "checkSamplesAfterGrouping"
+
+        when {
+            function {
+                """
+                input[0] = [
+                    [],
+                    [
+                        [ id: 'test', strandedness: 'unstranded', single_end: true ],
+                        [ id: 'test', strandedness: 'unstranded', single_end: false ]
+                    ],
+                    [
+                        [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ],
+                        [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.failed },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+    test("Test Function validateInputParameters success") {
+        // Needs more tests here to check for all options but there are a lot!
+
+        function "validateInputParameters"
+
+        when {
+            params {
+                fasta                  = "genome.fasta"
+                gtf                    = "genome.gtf"
+                gff                    = "genome.gff"
+                transcript_fasta       = "transcripts.fasta"
+                skip_bbsplit           = true
+                bbsplit_fasta_list     = null
+                remove_ribo_rna        = false
+                ribo_database_manifest = null
+                with_umi               = false
+                skip_umi_extract       = false
+                skip_alignment         = false
+                aligner                = "star"
+                skip_pseudo_alignment  = false
+                pseudo_aligner         = "salmon"
+                rsem_index             = "rsem_index"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function genomeExistsError finds genome") {
+
+        function "genomeExistsError"
+
+        when {
+            params {
+                genome = "myTest"
+                genomes {
+                    "myTest" {
+                        myAttribute = "myValue"
+                    }
+                }
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function genomeExistsError missing genome") {
+
+        function "genomeExistsError"
+
+        when {
+            params {
+                genome = "missingTest"
+                genomes {
+                    "myTest" {
+                        myAttribute = "myValue"
+                    }
+                }
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.failed },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+    test("Test Function toolCitationText") {
+
+        function "toolCitationText"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function toolBibliographyText") {
+
+        function "toolBibliographyText"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function gtfGffWarn") {
+
+        function "gtfGffWarn"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+
+    test("Test Function ncbiGenomeWarn") {
+
+        function "ncbiGenomeWarn"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+
+    test("Test Function ucscGenomeWarn") {
+
+        function "ucscGenomeWarn"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+
+    test("Test Function transcriptsFastaWarn") {
+
+        function "transcriptsFastaWarn"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+
+    test("Test Function skipAlignmentWarn") {
+
+        function "skipAlignmentWarn"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+
+    test("Test Function rsemUmiError") {
+
+        function "rsemUmiError"
+
+        then {
+            assertAll(
+                { assert function.failed },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+
+    test("Test Function rsemStarIndexWarn") {
+
+        function "rsemStarIndexWarn"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+    test("Test Function rsemStarExtraArgumentsWarn") {
+
+        function "rsemStarExtraArgumentsWarn"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+    test("Test Function additionaFastaIndexWarn") {
+
+        function "additionaFastaIndexWarn"
+
+        when {
+            function {
+                """
+                input[0] = "mockIndex"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function checkMaxContigSize") {
+
+        function "checkMaxContigSize"
+
+        when {
+            function {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+    test("Test Function getStarPercentMapped pass") {
+
+        function "getStarPercentMapped"
+
+        when {
+            function {
+                """
+                def alignLog = file("${workDir}/alignLog.txt")
+                alignLog.write("Uniquely mapped reads % | 95.6%")
+
+                input[0] = [
+                    min_mapped_reads: 1.0
+                ]
+                input[1] = alignLog
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert function.result == [ 95.6, true ] }
+            )
+        }
+
+    }
+
+    test("Test Function getStarPercentMapped fail") {
+
+        function "getStarPercentMapped"
+
+        when {
+            function {
+                """
+                def alignLog = file("${workDir}/alignLog.txt")
+                alignLog.write("Uniquely mapped reads % | 10.2%")
+
+                input[0] = [
+                    min_mapped_reads: 50.0
+                ]
+                input[1] = alignLog
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert function.result == [ 10.2, false ] }
+            )
+        }
+
+    }
+
+
+    test("Test Function biotypeInGtf success") {
+
+        function "biotypeInGtf"
+
+        when {
+            function {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[1] = "gene_biotype"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function biotypeInGtf failed") {
+
+        function "biotypeInGtf"
+
+        when {
+            function {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[1] = "NotAppearingInThisFile"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function getInferexperimentStrandedness reverse") {
+
+        function "getInferexperimentStrandedness"
+
+        when {
+            function {
+                """
+                def fileContents = [
+                    'This is PairEnd Data',
+                    'Fraction of reads failed to determine: 0.1565',
+                    'Fraction of reads explained by "1++,1--,2+-,2-+": 0.0075',
+                    'Fraction of reads explained by "1+-,1-+,2++,2--": 0.8361'
+                ]
+                def inferExperimentFile = file("${workDir}/inferExperimentFile.txt")
+                inferExperimentFile.withWriter{ out ->
+                    fileContents.each {out.println it}
+                }
+
+                input[0] = inferExperimentFile
+                input[1] = 0.8
+                input[2] = 0.1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test.snap b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test.snap
new file mode 100644
index 000000000..9deb0bca3
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,201 @@
+{
+    "Test Function gtfGffWarn": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:11.163299"
+    },
+    "Test Function biotypeInGtf success": {
+        "content": [
+            true
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:34:03.414382"
+    },
+    "Test Function toolBibliographyText": {
+        "content": [
+            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li> <li>Ewels, P., Magnusson, M., Lundin, S., & K\u00e4ller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047\u20133048. doi: /10.1093/bioinformatics/btw354</li>"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:07.698845"
+    },
+    "Test Function toolCitationText": {
+        "content": [
+            "Tools used in the workflow included: FastQC (Andrews 2010), MultiQC (Ewels et al. 2016) ."
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:04.677913"
+    },
+    "Test Function rsemUmiError": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:26.903306"
+    },
+    "Test Function checkSamplesAfterGrouping invalid strandedness": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:32:41.841561"
+    },
+    "Test Function biotypeInGtf failed": {
+        "content": [
+            false
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:34:07.750259"
+    },
+    "Test Function transcriptsFastaWarn": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:20.618971"
+    },
+    "Test Function ucscGenomeWarn": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:17.405648"
+    },
+    "Test Function skipAlignmentWarn": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:23.76368"
+    },
+    "Test Function checkMaxContigSize": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:40.548126"
+    },
+    "Test Function checkSamplesAfterGrouping success": {
+        "content": [
+            [
+                {
+                    "id": "test",
+                    "strandedness": "unstranded",
+                    "single_end": true
+                },
+                [
+                    [
+                        "/ngi-igenomes/testdata/nf-core/modules/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"
+                    ],
+                    [
+                        "/ngi-igenomes/testdata/nf-core/modules/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:32:37.450298"
+    },
+    "Test Function checkSamplesAfterGrouping invalid endedness": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:32:46.420194"
+    },
+    "Test Function genomeExistsError finds genome": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:32:58.626473"
+    },
+    "Test Function additionaFastaIndexWarn": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:36.224496"
+    },
+    "Test Function genomeExistsError missing genome": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:01.625542"
+    },
+    "Test Function ncbiGenomeWarn": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:14.286665"
+    },
+    "Test Function rsemStarExtraArgumentsWarn": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:33.141215"
+    },
+    "Test Function validateInputParameters success": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:32:49.565504"
+    },
+    "Test Function rsemStarIndexWarn": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-06T14:33:30.02058"
+    },
+    "Test Function getInferexperimentStrandedness reverse": {
+        "content": [
+            {
+                "inferred_strandedness": "reverse",
+                "forwardFragments": 0.749925006577425,
+                "reverseFragments": 83.60163982823676,
+                "unstrandedFragments": 15.64843516518582 
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-18T14:30:53.743529"
+    }
+}
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test
new file mode 100644
index 000000000..ea784ea01
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test
@@ -0,0 +1,35 @@
+nextflow_workflow {
+
+    name "Test Workflow PIPELINE_COMPLETION"
+    script "../main.nf"
+    workflow "PIPELINE_COMPLETION"
+
+    test("test PIPELINE_COMPLETION successfully completes") {
+
+        when {
+            workflow {
+                """
+                input[0] = "${projectDir}/nextflow_schema.json" // schema (string)
+                input[1] = null // email (string)
+                input[2] = null // email_on_fail (string)
+                input[3] = true // plaintext_email (boolean)
+                input[4] = "${outputDir}" // outputDir (string)
+                input[5] = true // monochrome_logs (boolean)
+                input[6] = null // hook_url (string)
+                input[7] = "${outputDir}/multiqc_report.html" // multiqc_report (string)
+                input[8] = Channel.of(['test_sample', true])
+                input[9] = Channel.of(['test_sample', true])
+                input[10] = Channel.of(['test_sample', true])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success}
+            )
+        }
+
+    }
+
+}
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test
new file mode 100644
index 000000000..c1db3fda8
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test
@@ -0,0 +1,50 @@
+nextflow_workflow {
+
+    name "Test Workflow PIPELINE_INITIALISATION"
+    script "../main.nf"
+    workflow "PIPELINE_INITIALISATION"
+
+    test("test PIPELINE_INITIALISATION successfully completes with valid parameters") {
+
+        when {
+            params {
+                // Genome references
+                fasta              = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta"
+                gtf                = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz"
+                gff                = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes.gff.gz"
+                transcript_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/transcriptome.fasta"
+                additional_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz"
+
+                bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txt"
+                hisat2_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/hisat2.tar.gz"
+                salmon_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gz"
+                rsem_index         = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/rsem.tar.gz"
+
+                // Other parameters
+                skip_bbsplit        = false
+                pseudo_aligner      = 'salmon'
+                umitools_bc_pattern = 'NNNN'
+                ribo_database_manifest = "${projectDir}/workflows/rnaseq/assets/rrna-db-defaults.txt"
+            }
+            workflow {
+                """
+                input[0] = false                               // version (boolean)
+                input[1] = false                               // help (boolean)
+                input[2] = "${projectDir}/nextflow_schema.json" // schema (string)
+                input[3] = true                                // validate_parameters (boolean)
+                input[4] = true                                // monochrome_logs (boolean)
+                input[5] = args                                // args (array)
+                input[6] = file("$outputDir")                   // outdir (string)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success}
+            )
+        }
+
+    }
+
+}
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
index 7c07084ff..fe6ff312f 100644
--- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
@@ -44,6 +44,7 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS {
 
     emit:
     bam      = UMITOOLS_DEDUP.out.bam          // channel: [ val(meta), path(bam) ]
+    deduplog = UMITOOLS_DEDUP.out.log          // channel: [ val(meta), path(log) ]
 
     bai      = SAMTOOLS_INDEX.out.bai          // channel: [ val(meta), path(bai) ]
     csi      = SAMTOOLS_INDEX.out.csi          // channel: [ val(meta), path(csi) ]
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml
index f11e7ab6f..93e1238b4 100644
--- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml
@@ -37,6 +37,10 @@ output:
       description: |
         CSI samtools index
         Structure: [ val(meta), path(csi) ]
+  - deduplog:
+      description: |
+        UMI-tools deduplication log
+        Structure: [ val(meta), path(log) ]
   - stats:
       description: |
         File containing samtools stats output
@@ -53,7 +57,9 @@ output:
       description: |
         Files containing software versions
         Structure: [ path(versions.yml) ]
-
 authors:
   - "@drpatelh"
   - "@KamilMaliszArdigen"
+maintainers:
+  - "@drpatelh"
+  - "@KamilMaliszArdigen"
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test
new file mode 100644
index 000000000..ab541cb88
--- /dev/null
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test
@@ -0,0 +1,66 @@
+nextflow_workflow {
+
+    name "Test Workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS"
+    script "../main.nf"
+    workflow "BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS"
+
+    test("sarscov2_bam_bai") {
+
+        when {
+            workflow {
+                """
+                val_get_dedup_stats = false
+
+                input[0] = Channel.of([
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = val_get_dedup_stats
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert workflow.out.deduplog.get(0).get(1) ==~ ".*.log"},
+                { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"},
+                { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"},
+                { assert snapshot(
+                    workflow.out.stats,
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2_bam_bai - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                val_get_dedup_stats = false
+
+                input[0] = Channel.of([
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = val_get_dedup_stats
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap
new file mode 100644
index 000000000..4fd70b5f3
--- /dev/null
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap
@@ -0,0 +1,169 @@
+{
+    "sarscov2_bam_bai": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.stats:md5,09d1bd8f10e000921202f7ea1cd0679e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.flagstat:md5,0bb716e40fae381b97484b58e0b16efe"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.idxstats:md5,1adb27b52d4d64b826f48b59d61dcd4d"
+                ]
+            ],
+            [
+                "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860",
+                "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4",
+                "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db",
+                "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69",
+                "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T11:53:11.53709"
+    },
+    "sarscov2_bam_bai - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860",
+                    "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4",
+                    "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db",
+                    "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69",
+                    "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+
+                ],
+                "deduplog": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860",
+                    "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4",
+                    "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db",
+                    "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69",
+                    "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:34:35.959581"
+    }
+}
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf
index 6e3df3320..2de059b84 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/main.nf
+++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf
@@ -9,7 +9,7 @@ include { BAM_STATS_SAMTOOLS    } from '../bam_stats_samtools/main'
 workflow BAM_MARKDUPLICATES_PICARD {
 
     take:
-    ch_bam   // channel: [ val(meta), path(bam) ]
+    ch_reads   // channel: [ val(meta), path(reads) ]
     ch_fasta // channel: [ path(fasta) ]
     ch_fai   // channel: [ path(fai) ]
 
@@ -17,31 +17,33 @@ workflow BAM_MARKDUPLICATES_PICARD {
 
     ch_versions = Channel.empty()
 
-    PICARD_MARKDUPLICATES ( ch_bam, ch_fasta, ch_fai )
+    PICARD_MARKDUPLICATES ( ch_reads, ch_fasta, ch_fai )
     ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions.first())
 
-    SAMTOOLS_INDEX ( PICARD_MARKDUPLICATES.out.bam )
+    ch_markdup = PICARD_MARKDUPLICATES.out.bam.mix(PICARD_MARKDUPLICATES.out.cram)
+
+    SAMTOOLS_INDEX ( ch_markdup )
     ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
 
-    ch_bam_bai = PICARD_MARKDUPLICATES.out.bam
-        .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true)
-        .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true)
-        .map {
-            meta, bam, bai, csi ->
-                if (bai) {
-                    [ meta, bam, bai ]
-                } else {
-                    [ meta, bam, csi ]
-                }
+    ch_reads_index = ch_markdup
+        .join(SAMTOOLS_INDEX.out.bai,  by: [0], remainder: true)
+        .join(SAMTOOLS_INDEX.out.crai, by: [0], remainder: true)
+        .join(SAMTOOLS_INDEX.out.csi,  by: [0], remainder: true)
+        .map{meta, reads, bai, crai, csi ->
+            if (bai) [ meta, reads, bai ]
+            else if (crai) [ meta, reads, crai ]
+            else [ meta, reads, csi ]
         }
 
-    BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta )
+    BAM_STATS_SAMTOOLS ( ch_reads_index, ch_fasta )
     ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions)
 
     emit:
     bam      = PICARD_MARKDUPLICATES.out.bam     // channel: [ val(meta), path(bam) ]
-    metrics  = PICARD_MARKDUPLICATES.out.metrics // channel: [ val(meta), path(bam) ]
+    cram     = PICARD_MARKDUPLICATES.out.cram    // channel: [ val(meta), path(cram) ]
+    metrics  = PICARD_MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ]
     bai      = SAMTOOLS_INDEX.out.bai            // channel: [ val(meta), path(bai) ]
+    crai     = SAMTOOLS_INDEX.out.crai           // channel: [ val(meta), path(crai) ]
     csi      = SAMTOOLS_INDEX.out.csi            // channel: [ val(meta), path(csi) ]
 
     stats    = BAM_STATS_SAMTOOLS.out.stats      // channel: [ val(meta), path(stats) ]
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml
index b924596d8..433d35b2b 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml
+++ b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml
@@ -6,7 +6,6 @@ keywords:
   - bam
   - sam
   - cram
-
 components:
   - picard/markduplicates
   - samtools/index
@@ -14,15 +13,14 @@ components:
   - samtools/idxstats
   - samtools/flagstat
   - bam_stats_samtools
-
 input:
-  - ch_bam:
+  - ch_reads:
       description: |
-        BAM/CRAM/SAM file
-        Structure: [ val(meta), path(bam) ]
+        Sequence reads in BAM/CRAM/SAM format
+        Structure: [ val(meta), path(reads) ]
   - ch_fasta:
       description: |
-        Reference genome fasta file
+        Reference genome fasta file required for CRAM input
         Structure: [ path(fasta) ]
   - ch_fasta:
       description: |
@@ -31,12 +29,20 @@ input:
 output:
   - bam:
       description: |
-        processed BAM/CRAM/SAM file
+        processed BAM/SAM file
         Structure: [ val(meta), path(bam) ]
   - bai:
       description: |
-        BAM/CRAM/SAM samtools index
+        BAM/SAM samtools index
         Structure: [ val(meta), path(bai) ]
+  - cram:
+      description: |
+        processed CRAM file
+        Structure: [ val(meta), path(cram) ]
+  - crai:
+      description: |
+        CRAM samtools index
+        Structure: [ val(meta), path(crai) ]
   - csi:
       description: |
         CSI samtools index
@@ -60,3 +66,6 @@ output:
 authors:
   - "@dmarron"
   - "@drpatelh"
+maintainers:
+  - "@dmarron"
+  - "@drpatelh"
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config b/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config
new file mode 100644
index 000000000..2778db78d
--- /dev/null
+++ b/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config
@@ -0,0 +1,41 @@
+if (!params.skip_alignment) {
+    if (!params.skip_markduplicates && !params.with_umi) {
+        process {
+            withName: '.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
+                ext.args   = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
+                ext.prefix = { "${meta.id}.markdup.sorted" }
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/picard_metrics" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*metrics.txt'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.bam'
+                    ]
+                ]
+            }
+
+            withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
+                ext.args   = { params.bam_csi_index ? '-c' : '' }
+                ext.prefix = { "${meta.id}.markdup.sorted" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.{bai,csi}'
+                ]
+            }
+
+            withName: '.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
+                ext.prefix = { "${meta.id}.markdup.sorted.bam" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.{stats,flagstat,idxstats}'
+                ]
+            }
+        }
+    }
+}
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test
new file mode 100644
index 000000000..f023a9f7d
--- /dev/null
+++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test
@@ -0,0 +1,142 @@
+nextflow_workflow {
+
+    name "Test Workflow BAM_MARKDUPLICATES_PICARD"
+    script "../main.nf"
+    workflow "BAM_MARKDUPLICATES_PICARD"
+
+    test("sarscov2 - bam") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("97") },
+                { assert snapshot(
+                    path(workflow.out.bam[0][1]),
+                    path(workflow.out.bai[0][1]),
+                    path(workflow.out.flagstat[0][1]),
+                    path(workflow.out.idxstats[0][1]),
+                    path(workflow.out.stats[0][1]),
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - cram") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("0.999986") },
+                { assert snapshot(
+                    file(workflow.out.cram[0][1]).name,
+                    path(workflow.out.crai[0][1]),
+                    path(workflow.out.flagstat[0][1]),
+                    path(workflow.out.idxstats[0][1]),
+                    path(workflow.out.stats[0][1]),
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - cram - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap
new file mode 100644
index 000000000..32788a18c
--- /dev/null
+++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap
@@ -0,0 +1,334 @@
+{
+    "homo_sapiens - cram": {
+        "content": [
+            "test.cram",
+            "test.cram.crai:md5,78d47ba01ac4e05f3ae1e353902a989e",
+            "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d",
+            "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15",
+            "test.stats:md5,372a7d9d9081aa009b21343a913beb14",
+            [
+                "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
+                "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
+                "versions.yml:md5,966dcea920866a87b55e665563864fc9",
+                "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                "versions.yml:md5,fcf804c605f455127f2449403d70390c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:28:15.15911"
+    },
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
+                    "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
+                    "versions.yml:md5,966dcea920866a87b55e665563864fc9",
+                    "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                    "versions.yml:md5,fcf804c605f455127f2449403d70390c"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
+                    "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
+                    "versions.yml:md5,966dcea920866a87b55e665563864fc9",
+                    "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                    "versions.yml:md5,fcf804c605f455127f2449403d70390c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:28:40.128144"
+    },
+    "homo_sapiens - cram - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
+                    "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
+                    "versions.yml:md5,966dcea920866a87b55e665563864fc9",
+                    "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                    "versions.yml:md5,fcf804c605f455127f2449403d70390c"
+                ],
+                "bai": [
+                    
+                ],
+                "bam": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "metrics": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
+                    "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
+                    "versions.yml:md5,966dcea920866a87b55e665563864fc9",
+                    "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                    "versions.yml:md5,fcf804c605f455127f2449403d70390c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:29:04.075263"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            "test.bam:md5,3091fe6ba1b7530f382fe40b9fd8f45b",
+            "test.bam.bai:md5,4d3ae8d013444b55e17aa0149a2ab404",
+            "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783",
+            "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2",
+            "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574",
+            [
+                "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
+                "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
+                "versions.yml:md5,966dcea920866a87b55e665563864fc9",
+                "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                "versions.yml:md5,fcf804c605f455127f2449403d70390c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:27:47.343274"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_rseqc/main.nf b/subworkflows/nf-core/bam_rseqc/main.nf
index a698b30ab..043321a13 100644
--- a/subworkflows/nf-core/bam_rseqc/main.nf
+++ b/subworkflows/nf-core/bam_rseqc/main.nf
@@ -13,44 +13,46 @@ include { RSEQC_TIN                } from '../../../modules/nf-core/rseqc/tin/ma
 
 workflow BAM_RSEQC {
     take:
-    ch_bam_bai    // channel: [ val(meta), [ bam, bai ] ]
-    ch_bed        //    file: /path/to/genome.bed
+    bam_bai       // channel: [ val(meta), [ bam, bai ] ]
+    bed           // channel: [ genome.bed ]
     rseqc_modules //    list: rseqc modules to run
 
     main:
 
-    ch_versions = Channel.empty()
+    bam = bam_bai.map{ [ it[0], it[1] ] }
 
-    ch_bam_bai
-        .map { [ it[0], it[1] ] }
-        .set { ch_bam }
+    versions = Channel.empty()
 
     //
     // Run RSeQC bam_stat.py
     //
     bamstat_txt = Channel.empty()
+
     if ('bam_stat' in rseqc_modules) {
-        RSEQC_BAMSTAT ( ch_bam )
+        RSEQC_BAMSTAT(bam)
         bamstat_txt = RSEQC_BAMSTAT.out.txt
-        ch_versions = ch_versions.mix(RSEQC_BAMSTAT.out.versions.first())
+        versions    = versions.mix(RSEQC_BAMSTAT.out.versions.first())
     }
 
     //
     // Run RSeQC inner_distance.py
     //
+    innerdistance_all      = Channel.empty()
     innerdistance_distance = Channel.empty()
     innerdistance_freq     = Channel.empty()
     innerdistance_mean     = Channel.empty()
     innerdistance_pdf      = Channel.empty()
     innerdistance_rscript  = Channel.empty()
+
     if ('inner_distance' in rseqc_modules) {
-        RSEQC_INNERDISTANCE ( ch_bam, ch_bed )
+        RSEQC_INNERDISTANCE(bam, bed)
         innerdistance_distance = RSEQC_INNERDISTANCE.out.distance
         innerdistance_freq     = RSEQC_INNERDISTANCE.out.freq
         innerdistance_mean     = RSEQC_INNERDISTANCE.out.mean
         innerdistance_pdf      = RSEQC_INNERDISTANCE.out.pdf
         innerdistance_rscript  = RSEQC_INNERDISTANCE.out.rscript
-        ch_versions = ch_versions.mix(RSEQC_INNERDISTANCE.out.versions.first())
+        innerdistance_all      = innerdistance_distance.mix(innerdistance_freq, innerdistance_mean, innerdistance_pdf, innerdistance_rscript)
+        versions               = versions.mix(RSEQC_INNERDISTANCE.out.versions.first())
     }
 
     //
@@ -58,14 +60,15 @@ workflow BAM_RSEQC {
     //
     inferexperiment_txt = Channel.empty()
     if ('infer_experiment' in rseqc_modules) {
-        RSEQC_INFEREXPERIMENT ( ch_bam, ch_bed )
+        RSEQC_INFEREXPERIMENT(bam, bed)
         inferexperiment_txt = RSEQC_INFEREXPERIMENT.out.txt
-        ch_versions = ch_versions.mix(RSEQC_INFEREXPERIMENT.out.versions.first())
+        versions            = versions.mix(RSEQC_INFEREXPERIMENT.out.versions.first())
     }
 
     //
     // Run RSeQC junction_annotation.py
     //
+    junctionannotation_all          = Channel.empty()
     junctionannotation_bed          = Channel.empty()
     junctionannotation_interact_bed = Channel.empty()
     junctionannotation_xls          = Channel.empty()
@@ -73,8 +76,9 @@ workflow BAM_RSEQC {
     junctionannotation_events_pdf   = Channel.empty()
     junctionannotation_rscript      = Channel.empty()
     junctionannotation_log          = Channel.empty()
+
     if ('junction_annotation' in rseqc_modules) {
-        RSEQC_JUNCTIONANNOTATION ( ch_bam, ch_bed )
+        RSEQC_JUNCTIONANNOTATION(bam, bed)
         junctionannotation_bed          = RSEQC_JUNCTIONANNOTATION.out.bed
         junctionannotation_interact_bed = RSEQC_JUNCTIONANNOTATION.out.interact_bed
         junctionannotation_xls          = RSEQC_JUNCTIONANNOTATION.out.xls
@@ -82,60 +86,70 @@ workflow BAM_RSEQC {
         junctionannotation_events_pdf   = RSEQC_JUNCTIONANNOTATION.out.events_pdf
         junctionannotation_rscript      = RSEQC_JUNCTIONANNOTATION.out.rscript
         junctionannotation_log          = RSEQC_JUNCTIONANNOTATION.out.log
-        ch_versions = ch_versions.mix(RSEQC_JUNCTIONANNOTATION.out.versions.first())
+        junctionannotation_all          = junctionannotation_bed.mix(junctionannotation_interact_bed, junctionannotation_xls, junctionannotation_pdf, junctionannotation_events_pdf, junctionannotation_rscript, junctionannotation_log)
+        versions                        = versions.mix(RSEQC_JUNCTIONANNOTATION.out.versions.first())
     }
 
     //
     // Run RSeQC junction_saturation.py
     //
+    junctionsaturation_all     = Channel.empty()
     junctionsaturation_pdf     = Channel.empty()
     junctionsaturation_rscript = Channel.empty()
+
     if ('junction_saturation' in rseqc_modules) {
-        RSEQC_JUNCTIONSATURATION ( ch_bam, ch_bed )
+        RSEQC_JUNCTIONSATURATION(bam, bed)
         junctionsaturation_pdf     = RSEQC_JUNCTIONSATURATION.out.pdf
         junctionsaturation_rscript = RSEQC_JUNCTIONSATURATION.out.rscript
-        ch_versions = ch_versions.mix(RSEQC_JUNCTIONSATURATION.out.versions.first())
+        junctionsaturation_all     = junctionsaturation_pdf.mix(junctionsaturation_rscript)
+        versions                   = versions.mix(RSEQC_JUNCTIONSATURATION.out.versions.first())
     }
 
     //
     // Run RSeQC read_distribution.py
     //
     readdistribution_txt = Channel.empty()
+
     if ('read_distribution' in rseqc_modules) {
-        RSEQC_READDISTRIBUTION ( ch_bam, ch_bed )
+        RSEQC_READDISTRIBUTION(bam, bed)
         readdistribution_txt = RSEQC_READDISTRIBUTION.out.txt
-        ch_versions = ch_versions.mix(RSEQC_READDISTRIBUTION.out.versions.first())
+        versions            = versions.mix(RSEQC_READDISTRIBUTION.out.versions.first())
     }
 
     //
     // Run RSeQC read_duplication.py
     //
+    readduplication_all     = Channel.empty()
     readduplication_seq_xls = Channel.empty()
     readduplication_pos_xls = Channel.empty()
     readduplication_pdf     = Channel.empty()
     readduplication_rscript = Channel.empty()
+
     if ('read_duplication' in rseqc_modules) {
-        RSEQC_READDUPLICATION ( ch_bam )
+        RSEQC_READDUPLICATION(bam )
         readduplication_seq_xls = RSEQC_READDUPLICATION.out.seq_xls
         readduplication_pos_xls = RSEQC_READDUPLICATION.out.pos_xls
         readduplication_pdf     = RSEQC_READDUPLICATION.out.pdf
         readduplication_rscript = RSEQC_READDUPLICATION.out.rscript
-        ch_versions = ch_versions.mix(RSEQC_READDUPLICATION.out.versions.first())
+        readduplication_all     = readduplication_seq_xls.mix(readduplication_pos_xls, readduplication_pdf, readduplication_rscript)
+        versions                = versions.mix(RSEQC_READDUPLICATION.out.versions.first())
     }
 
     //
     // Run RSeQC tin.py
     //
     tin_txt = Channel.empty()
+
     if ('tin' in rseqc_modules) {
-        RSEQC_TIN ( ch_bam_bai, ch_bed )
-        tin_txt     = RSEQC_TIN.out.txt
-        ch_versions = ch_versions.mix(RSEQC_TIN.out.versions.first())
+        RSEQC_TIN(bam_bai, bed)
+        tin_txt      = RSEQC_TIN.out.txt
+        versions    = versions.mix(RSEQC_TIN.out.versions.first())
     }
 
     emit:
     bamstat_txt                     // channel: [ val(meta), txt ]
 
+    innerdistance_all               // channel: [ val(meta), {txt, pdf, r} ]
     innerdistance_distance          // channel: [ val(meta), txt ]
     innerdistance_freq              // channel: [ val(meta), txt ]
     innerdistance_mean              // channel: [ val(meta), txt ]
@@ -144,6 +158,7 @@ workflow BAM_RSEQC {
 
     inferexperiment_txt             // channel: [ val(meta), txt ]
 
+    junctionannotation_all          // channel: [ val(meta), {bed, xls, pdf, r, log} ]
     junctionannotation_bed          // channel: [ val(meta), bed ]
     junctionannotation_interact_bed // channel: [ val(meta), bed ]
     junctionannotation_xls          // channel: [ val(meta), xls ]
@@ -152,11 +167,13 @@ workflow BAM_RSEQC {
     junctionannotation_rscript      // channel: [ val(meta), r   ]
     junctionannotation_log          // channel: [ val(meta), log ]
 
+    junctionsaturation_all          // channel: [ val(meta), {pdf, r} ]
     junctionsaturation_pdf          // channel: [ val(meta), pdf ]
     junctionsaturation_rscript      // channel: [ val(meta), r   ]
 
     readdistribution_txt            // channel: [ val(meta), txt ]
 
+    readduplication_all             // channel: [ val(meta), {xls, pdf, r} ]
     readduplication_seq_xls         // channel: [ val(meta), xls ]
     readduplication_pos_xls         // channel: [ val(meta), xls ]
     readduplication_pdf             // channel: [ val(meta), pdf ]
@@ -164,5 +181,5 @@ workflow BAM_RSEQC {
 
     tin_txt                         // channel: [ val(meta), txt ]
 
-    versions = ch_versions          // channel: [ versions.yml ]
+    versions                        // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/bam_rseqc/meta.yml b/subworkflows/nf-core/bam_rseqc/meta.yml
index 428b83e6d..6e76ff560 100644
--- a/subworkflows/nf-core/bam_rseqc/meta.yml
+++ b/subworkflows/nf-core/bam_rseqc/meta.yml
@@ -12,8 +12,16 @@ keywords:
   - readdistribution
   - readduplication
   - tin
-modules:
+components:
   - rseqc
+  - rseqc/tin
+  - rseqc/readduplication
+  - rseqc/readdistribution
+  - rseqc/junctionsaturation
+  - rseqc/junctionannotation
+  - rseqc/innerdistance
+  - rseqc/inferexperiment
+  - rseqc/bamstat
 input:
   - meta:
       type: map
@@ -42,6 +50,10 @@ output:
       type: file
       description: bam statistics report
       pattern: "*.bam_stat.txt"
+  - innerdistance_all:
+      type: file
+      description: All the output files from RSEQC_INNERDISTANCE
+      pattern: "*.{txt,pdf,R}"
   - innerdistance_distance:
       type: file
       description: the inner distances
@@ -66,6 +78,10 @@ output:
       type: file
       description: infer_experiment results report
       pattern: "*.infer_experiment.txt"
+  - junctionannotation_all:
+      type: file
+      description: All the output files from RSEQC_JUNCTIONANNOTATION
+      pattern: "*.{bed,xls,pdf,R,log}"
   - junctionannotation_bed:
       type: file
       description: bed file of annotated junctions
@@ -94,6 +110,10 @@ output:
       type: file
       description: Log file generated by tool
       pattern: "*.log"
+  - junctionsaturation_all:
+      type: file
+      description: All the output files from RSEQC_JUNCTIONSATURATION
+      pattern: "*.{pdf,R}"
   - junctionsaturation_pdf:
       type: file
       description: Junction saturation report
@@ -106,6 +126,10 @@ output:
       type: file
       description: the read distribution report
       pattern: "*.read_distribution.txt"
+  - readduplication_all:
+      type: file
+      description: All the output files from RSEQC_READDUPLICATION
+      pattern: "*.{xls,pdf,R}"
   - readduplication_seq_xls:
       type: file
       description: Read duplication rate determined from mapping position of read
@@ -133,3 +157,6 @@ output:
 authors:
   - "@drpatelh"
   - "@kevinmenden"
+maintainers:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/subworkflows/nf-core/bam_rseqc/nextflow.config b/subworkflows/nf-core/bam_rseqc/nextflow.config
new file mode 100644
index 000000000..4fabc8e99
--- /dev/null
+++ b/subworkflows/nf-core/bam_rseqc/nextflow.config
@@ -0,0 +1,153 @@
+def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
+
+if (!params.skip_alignment && !params.skip_qc && !params.skip_rseqc) {
+    if ('bam_stat' in rseqc_modules) {
+        process {
+            withName: '.*:BAM_RSEQC:RSEQC_BAMSTAT' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+
+    if ('infer_experiment' in rseqc_modules) {
+        process {
+            withName: '.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+
+    if ('junction_annotation' in rseqc_modules) {
+        process {
+            withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION' {
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/pdf" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.pdf'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/bed" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.bed'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/xls" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.xls'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/log" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/rscript" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.r'
+                    ]
+                ]
+            }
+        }
+    }
+
+    if ('junction_saturation' in rseqc_modules) {
+        process {
+            withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONSATURATION' {
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/pdf" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.pdf'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/rscript" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.r'
+                    ]
+                ]
+            }
+        }
+    }
+
+    if ('read_duplication' in rseqc_modules) {
+        process {
+            withName: '.*:BAM_RSEQC:RSEQC_READDUPLICATION' {
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/pdf" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.pdf'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/xls" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.xls'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/rscript" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.r'
+                    ]
+                ]
+            }
+        }
+    }
+
+    if ('read_distribution' in rseqc_modules && !params.bam_csi_index) {
+        process {
+            withName: '.*:BAM_RSEQC:RSEQC_READDISTRIBUTION' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+
+    if ('inner_distance' in rseqc_modules && !params.bam_csi_index) {
+        process {
+            withName: '.*:BAM_RSEQC:RSEQC_INNERDISTANCE' {
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.txt',
+                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/pdf" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.pdf'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/rscript" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.r'
+                    ]
+                ]
+            }
+        }
+    }
+
+    if ('tin' in rseqc_modules && !params.bam_csi_index) {
+        process {
+            withName: '.*:BAM_RSEQC:RSEQC_TIN' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+}
diff --git a/subworkflows/nf-core/bam_rseqc/tests/main.nf.test b/subworkflows/nf-core/bam_rseqc/tests/main.nf.test
new file mode 100644
index 000000000..492cfb6fe
--- /dev/null
+++ b/subworkflows/nf-core/bam_rseqc/tests/main.nf.test
@@ -0,0 +1,134 @@
+nextflow_workflow {
+
+    name "Test Workflow BAM_RSEQC"
+    script "../main.nf"
+    workflow "BAM_RSEQC"
+
+    test("sarscov2 paired-end [bam]") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true)
+                ])
+                input[2] = ['bam_stat', 'inner_distance', 'infer_experiment', 'junction_annotation', 'junction_saturation', 'read_distribution', 'read_duplication', 'tin']
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert workflow.out.innerdistance_all.any { it[1].endsWith('.pdf') && file(it[1]).exists() } },
+                { assert workflow.out.readduplication_all.any { it[1].endsWith('.pdf') && file(it[1]).exists() } },
+                { assert workflow.out.junctionsaturation_all.any { it[1].endsWith('.pdf') && file(it[1]).exists() } },
+                { assert snapshot(
+                    workflow.out.bamstat_txt,
+                    workflow.out.innerdistance_all.findAll { it[1].endsWith('.pdf') == false },
+                    workflow.out.inferexperiment_txt,
+                    workflow.out.junctionannotation_all.findAll { it[1].endsWith('.xls') == false && it[1].endsWith('.r') == false },
+                    workflow.out.junctionsaturation_all.findAll { it[1].endsWith('.pdf') == false },
+                    workflow.out.readdistribution_txt,
+                    workflow.out.readduplication_all.findAll { it[1].endsWith('.pdf') == false },
+                    workflow.out.tin_txt,
+                    workflow.out.versions).match()}
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] no modules") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true)
+                ])
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.bamstat_txt.size() == 0 },
+                { assert workflow.out.innerdistance_all.size() == 0 },
+                { assert workflow.out.inferexperiment_txt.size() == 0 },
+                { assert workflow.out.junctionannotation_all.size() == 0 },
+                { assert workflow.out.junctionsaturation_all.size() == 0 },
+                { assert workflow.out.readdistribution_txt.size() == 0 },
+                { assert workflow.out.readduplication_all.size() == 0 },
+                { assert workflow.out.tin_txt.size() == 0 },
+                { assert workflow.out.versions.size() == 0 }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true)
+                ])
+                input[2] = ['bam_stat', 'inner_distance', 'infer_experiment', 'junction_annotation', 'junction_saturation', 'read_distribution', 'read_duplication', 'tin']
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] no modules - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true)
+                ])
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/bam_rseqc/tests/main.nf.test.snap b/subworkflows/nf-core/bam_rseqc/tests/main.nf.test.snap
new file mode 100644
index 000000000..0040810cc
--- /dev/null
+++ b/subworkflows/nf-core/bam_rseqc/tests/main.nf.test.snap
@@ -0,0 +1,903 @@
+{
+    "sarscov2 paired-end [bam]": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bam_stat.txt:md5,2675857864c1d1139b2a19d25dc36b09"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.inner_distance.txt:md5,a1acc9def0f64a5500d4c4cb47cbe32b"
+                ],
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.inner_distance_freq.txt:md5,3fc037501f5899b5da009c8ce02fc25e"
+                ],
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.inner_distance_mean.txt:md5,58398b7d5a29a5e564f9e3c50b55996c"
+                ],
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.inner_distance_plot.r:md5,5859fbd5b42046d47e8b9aa85077f4ea"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.infer_experiment.txt:md5,f9d0bfc239df637cd8aeda40ade3c59a"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.junction_annotation.log:md5,d75e0f5d62fada8aa9449991b209554c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.junctionSaturation_plot.r:md5,caa6e63dcb477aabb169882b2f30dadd"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.read_distribution.txt:md5,56893fdc0809d968629a363551a1655f"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.DupRate_plot.r:md5,3c0325095cee4835b921e57d61c23dca"
+                ],
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.pos.DupRate.xls:md5,a859bc2031d46bf1cc4336205847caa3"
+                ],
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.seq.DupRate.xls:md5,ee8783399eec5a18522a6f08bece338b"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.paired_end.sorted.summary.txt:md5,9d98447e178b89a89f6f5aba7a772fe6"
+                ]
+            ],
+            [
+                "versions.yml:md5,60dc1afce7fecb7270e998a00ee393e2",
+                "versions.yml:md5,9bc3caee6aeb54f23f5296b499546515",
+                "versions.yml:md5,a25161998ca60d5ce4e9a86abbf1bcb8",
+                "versions.yml:md5,c175b92f50b5be38a8808cbf7ac7452e",
+                "versions.yml:md5,ca7e95cf7ff7cff5d052b890729f7ead",
+                "versions.yml:md5,d03beea3c68934c3f3623a005c1424d2",
+                "versions.yml:md5,f2f3ecd549045f7595245f904f5d9414",
+                "versions.yml:md5,fd16f1098b9c285f3ea7bd3daf4e8f10"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:07:54.452949"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam_stat.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_mean.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.Interact.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "13": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.events.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "14": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "15": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction_annotation.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "16": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junctionSaturation_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junctionSaturation_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "17": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junctionSaturation_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "18": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junctionSaturation_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "19": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.read_distribution.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "20": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.DupRate_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.DupRate_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pos.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.seq.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "21": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.seq.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "22": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pos.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "23": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.DupRate_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "24": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.DupRate_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "25": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.paired_end.sorted.bam.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "26": [
+                    "versions.yml:md5,60dc1afce7fecb7270e998a00ee393e2",
+                    "versions.yml:md5,9bc3caee6aeb54f23f5296b499546515",
+                    "versions.yml:md5,a25161998ca60d5ce4e9a86abbf1bcb8",
+                    "versions.yml:md5,c175b92f50b5be38a8808cbf7ac7452e",
+                    "versions.yml:md5,ca7e95cf7ff7cff5d052b890729f7ead",
+                    "versions.yml:md5,d03beea3c68934c3f3623a005c1424d2",
+                    "versions.yml:md5,f2f3ecd549045f7595245f904f5d9414",
+                    "versions.yml:md5,fd16f1098b9c285f3ea7bd3daf4e8f10"
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_mean.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.infer_experiment.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.Interact.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.events.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction_annotation.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bamstat_txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam_stat.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "inferexperiment_txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.infer_experiment.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "innerdistance_all": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_mean.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "innerdistance_distance": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "innerdistance_freq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_freq.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "innerdistance_mean": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_mean.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "innerdistance_pdf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "innerdistance_rscript": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.inner_distance_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionannotation_all": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.Interact.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.events.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction_annotation.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionannotation_bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionannotation_events_pdf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.events.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionannotation_interact_bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.Interact.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionannotation_log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction_annotation.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionannotation_pdf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionannotation_rscript": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionannotation_xls": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junction.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionsaturation_all": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junctionSaturation_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junctionSaturation_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionsaturation_pdf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junctionSaturation_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junctionsaturation_rscript": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junctionSaturation_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "readdistribution_txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.read_distribution.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "readduplication_all": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.DupRate_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.DupRate_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pos.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.seq.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "readduplication_pdf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.DupRate_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "readduplication_pos_xls": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pos.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "readduplication_rscript": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.DupRate_plot.r:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "readduplication_seq_xls": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.seq.DupRate.xls:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tin_txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.paired_end.sorted.bam.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,60dc1afce7fecb7270e998a00ee393e2",
+                    "versions.yml:md5,9bc3caee6aeb54f23f5296b499546515",
+                    "versions.yml:md5,a25161998ca60d5ce4e9a86abbf1bcb8",
+                    "versions.yml:md5,c175b92f50b5be38a8808cbf7ac7452e",
+                    "versions.yml:md5,ca7e95cf7ff7cff5d052b890729f7ead",
+                    "versions.yml:md5,d03beea3c68934c3f3623a005c1424d2",
+                    "versions.yml:md5,f2f3ecd549045f7595245f904f5d9414",
+                    "versions.yml:md5,fd16f1098b9c285f3ea7bd3daf4e8f10"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:08:17.304769"
+    },
+    "sarscov2 paired-end [bam] no modules - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "10": [
+                    
+                ],
+                "11": [
+                    
+                ],
+                "12": [
+                    
+                ],
+                "13": [
+                    
+                ],
+                "14": [
+                    
+                ],
+                "15": [
+                    
+                ],
+                "16": [
+                    
+                ],
+                "17": [
+                    
+                ],
+                "18": [
+                    
+                ],
+                "19": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "20": [
+                    
+                ],
+                "21": [
+                    
+                ],
+                "22": [
+                    
+                ],
+                "23": [
+                    
+                ],
+                "24": [
+                    
+                ],
+                "25": [
+                    
+                ],
+                "26": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    
+                ],
+                "8": [
+                    
+                ],
+                "9": [
+                    
+                ],
+                "bamstat_txt": [
+                    
+                ],
+                "inferexperiment_txt": [
+                    
+                ],
+                "innerdistance_all": [
+                    
+                ],
+                "innerdistance_distance": [
+                    
+                ],
+                "innerdistance_freq": [
+                    
+                ],
+                "innerdistance_mean": [
+                    
+                ],
+                "innerdistance_pdf": [
+                    
+                ],
+                "innerdistance_rscript": [
+                    
+                ],
+                "junctionannotation_all": [
+                    
+                ],
+                "junctionannotation_bed": [
+                    
+                ],
+                "junctionannotation_events_pdf": [
+                    
+                ],
+                "junctionannotation_interact_bed": [
+                    
+                ],
+                "junctionannotation_log": [
+                    
+                ],
+                "junctionannotation_pdf": [
+                    
+                ],
+                "junctionannotation_rscript": [
+                    
+                ],
+                "junctionannotation_xls": [
+                    
+                ],
+                "junctionsaturation_all": [
+                    
+                ],
+                "junctionsaturation_pdf": [
+                    
+                ],
+                "junctionsaturation_rscript": [
+                    
+                ],
+                "readdistribution_txt": [
+                    
+                ],
+                "readduplication_all": [
+                    
+                ],
+                "readduplication_pdf": [
+                    
+                ],
+                "readduplication_pos_xls": [
+                    
+                ],
+                "readduplication_rscript": [
+                    
+                ],
+                "readduplication_seq_xls": [
+                    
+                ],
+                "tin_txt": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:08:24.443731"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
index fc1c652b9..b716375b0 100644
--- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
@@ -15,7 +15,7 @@ workflow BAM_SORT_STATS_SAMTOOLS {
 
     ch_versions = Channel.empty()
 
-    SAMTOOLS_SORT ( ch_bam )
+    SAMTOOLS_SORT ( ch_bam, ch_fasta )
     ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first())
 
     SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam )
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
index 69c16be41..e01f9ccf6 100644
--- a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
@@ -65,3 +65,6 @@ output:
 authors:
   - "@drpatelh"
   - "@ewels"
+maintainers:
+  - "@drpatelh"
+  - "@ewels"
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test
new file mode 100644
index 000000000..a21782114
--- /dev/null
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test
@@ -0,0 +1,122 @@
+nextflow_workflow {
+
+    name "Test Workflow BAM_SORT_STATS_SAMTOOLS"
+    script "../main.nf"
+    workflow "BAM_SORT_STATS_SAMTOOLS"
+
+    test("test_bam_sort_stats_samtools_single_end") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"},
+                { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"},
+                { assert snapshot(
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.stats,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_bam_sort_stats_samtools_paired_end") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"},
+                { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"},
+                { assert snapshot(
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.stats,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_bam_sort_stats_samtools_single_end - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("test_bam_sort_stats_samtools_paired_end - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap
new file mode 100644
index 000000000..b7f4da177
--- /dev/null
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap
@@ -0,0 +1,330 @@
+{
+    "test_bam_sort_stats_samtools_single_end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.stats:md5,d32de3b3716a11039cef2367c3c1a56e"
+                ]
+            ],
+            [
+                "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1",
+                "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4",
+                "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1",
+                "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30",
+                "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:02:44.34964"
+    },
+    "test_bam_sort_stats_samtools_paired_end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574"
+                ]
+            ],
+            [
+                "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1",
+                "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4",
+                "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1",
+                "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30",
+                "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:03:02.583095"
+    },
+    "test_bam_sort_stats_samtools_single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1",
+                    "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4",
+                    "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1",
+                    "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30",
+                    "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1",
+                    "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4",
+                    "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1",
+                    "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30",
+                    "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:03:22.328703"
+    },
+    "test_bam_sort_stats_samtools_paired_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1",
+                    "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4",
+                    "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1",
+                    "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30",
+                    "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1",
+                    "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4",
+                    "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1",
+                    "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30",
+                    "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:03:38.833662"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml
index 87863b11b..809bf736b 100644
--- a/subworkflows/nf-core/bam_stats_samtools/meta.yml
+++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml
@@ -39,3 +39,5 @@ output:
         Structure: [ path(versions.yml) ]
 authors:
   - "@drpatelh"
+maintainers:
+  - "@drpatelh"
diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test
new file mode 100644
index 000000000..4597aea27
--- /dev/null
+++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test
@@ -0,0 +1,180 @@
+nextflow_workflow {
+
+    name "Test Workflow BAM_STATS_SAMTOOLS"
+    script "../main.nf"
+    workflow "BAM_STATS_SAMTOOLS"
+
+    test("test_bam_stats_samtools_single_end") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.stats,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_bam_stats_samtools_paired_end") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.stats,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_bam_stats_samtools_paired_end_cram") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.stats,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test ("test_bam_stats_samtools_single_end - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("test_bam_stats_samtools_paired_end - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("test_bam_stats_samtools_paired_end_cram - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap
new file mode 100644
index 000000000..a3ddcc5ce
--- /dev/null
+++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap
@@ -0,0 +1,350 @@
+{
+    "test_bam_stats_samtools_paired_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,3c485730f712b115bcdc235e7294133b",
+                    "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e",
+                    "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3"
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3c485730f712b115bcdc235e7294133b",
+                    "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e",
+                    "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:20:06.699297"
+    },
+    "test_bam_stats_samtools_single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,3c485730f712b115bcdc235e7294133b",
+                    "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e",
+                    "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3"
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3c485730f712b115bcdc235e7294133b",
+                    "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e",
+                    "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:19:57.708621"
+    },
+    "test_bam_stats_samtools_paired_end_cram - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,3c485730f712b115bcdc235e7294133b",
+                    "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e",
+                    "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3"
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3c485730f712b115bcdc235e7294133b",
+                    "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e",
+                    "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:20:17.051493"
+    },
+    "test_bam_stats_samtools_single_end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.stats:md5,4a0c429c661d6aa0b60acb9309da642d"
+                ]
+            ],
+            [
+                "versions.yml:md5,3c485730f712b115bcdc235e7294133b",
+                "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e",
+                "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:19:25.801394"
+    },
+    "test_bam_stats_samtools_paired_end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.stats:md5,7afd486ad6abb9a2a3dac90c99e1d87b"
+                ]
+            ],
+            [
+                "versions.yml:md5,3c485730f712b115bcdc235e7294133b",
+                "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e",
+                "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:19:36.158768"
+    },
+    "test_bam_stats_samtools_paired_end_cram": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.flagstat:md5,a53f3d26e2e9851f7d528442bbfe9781"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.stats:md5,16b59a1f2c99d9fe30f711adc3ebe32d"
+                ]
+            ],
+            [
+                "versions.yml:md5,3c485730f712b115bcdc235e7294133b",
+                "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e",
+                "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:19:46.625907"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml
index 5ad4db7db..49b9c27a1 100644
--- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml
+++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml
@@ -34,3 +34,6 @@ output:
 authors:
   - "@drpatelh"
   - "@KamilMaliszArdigen"
+maintainers:
+  - "@drpatelh"
+  - "@KamilMaliszArdigen"
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test
new file mode 100644
index 000000000..17ec676ca
--- /dev/null
+++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test
@@ -0,0 +1,53 @@
+nextflow_workflow {
+
+    name "Test Workflow BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG"
+    script "../main.nf"
+    workflow "BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG"
+    config "./nextflow.config"
+
+    test("sarscov2 [bedgraph] [genome_sizes]") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bedgraph/test.bedgraph', checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 [bedgraph] [genome_sizes] - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bedgraph/test.bedgraph', checkIfExists: true)
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap
new file mode 100644
index 000000000..26ed39c00
--- /dev/null
+++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap
@@ -0,0 +1,112 @@
+{
+    "sarscov2 [bedgraph] [genome_sizes]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bigWig:md5,910ecc7f57e3bbd5fac5a8edba4f615d"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.clip.bedGraph:md5,e02395e1f7c593b3f79563067159ebc2"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,21c57fc724b374139b11f88017251733",
+                    "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f"
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.clip.bedGraph:md5,e02395e1f7c593b3f79563067159ebc2"
+                    ]
+                ],
+                "bigwig": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bigWig:md5,910ecc7f57e3bbd5fac5a8edba4f615d"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,21c57fc724b374139b11f88017251733",
+                    "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2023-11-26T01:55:31.016058335"
+    },
+    "sarscov2 [bedgraph] [genome_sizes] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bigWig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.clip.bedGraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,21c57fc724b374139b11f88017251733",
+                    "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f"
+                ],
+                "bedgraph": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.clip.bedGraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bigwig": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bigWig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,21c57fc724b374139b11f88017251733",
+                    "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:22:51.388076"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/nextflow.config b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/nextflow.config
new file mode 100644
index 000000000..46af4b0a9
--- /dev/null
+++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: UCSC_BEDCLIP {
+        ext.prefix = { "${meta.id}.clip" }
+    }
+
+}
diff --git a/subworkflows/nf-core/fastq_align_hisat2/main.nf b/subworkflows/nf-core/fastq_align_hisat2/main.nf
index a2ec1cf5e..511fe035c 100644
--- a/subworkflows/nf-core/fastq_align_hisat2/main.nf
+++ b/subworkflows/nf-core/fastq_align_hisat2/main.nf
@@ -41,4 +41,3 @@ workflow FASTQ_ALIGN_HISAT2 {
 
     versions = ch_versions                          // channel: [ versions.yml ]
 }
-
diff --git a/subworkflows/nf-core/fastq_align_hisat2/meta.yml b/subworkflows/nf-core/fastq_align_hisat2/meta.yml
index 2b05beb68..6f00d4daa 100644
--- a/subworkflows/nf-core/fastq_align_hisat2/meta.yml
+++ b/subworkflows/nf-core/fastq_align_hisat2/meta.yml
@@ -87,3 +87,5 @@ output:
       pattern: "versions.yml"
 authors:
   - "@priyanka-surana"
+maintainers:
+  - "@priyanka-surana"
diff --git a/subworkflows/nf-core/fastq_align_hisat2/nextflow.config b/subworkflows/nf-core/fastq_align_hisat2/nextflow.config
new file mode 100644
index 000000000..0f6d1abdc
--- /dev/null
+++ b/subworkflows/nf-core/fastq_align_hisat2/nextflow.config
@@ -0,0 +1,26 @@
+if (!params.skip_alignment && params.aligner == 'hisat2') {
+    process {
+        withName: '.*:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN' {
+            ext.args   = '--met-stderr --new-summary --dta'
+            publishDir = [
+                [
+                    path: { "${params.outdir}/${params.aligner}/log" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.log'
+                ],
+                [
+                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bam',
+                    saveAs: { params.save_align_intermeds ? it : null }
+                ],
+                [
+                    path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.fastq.gz',
+                    saveAs: { params.save_unaligned ? it : null }
+                ]
+            ]
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test
new file mode 100644
index 000000000..0048b3b33
--- /dev/null
+++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test
@@ -0,0 +1,207 @@
+nextflow_workflow {
+
+    name "Test Subworkflow FASTQ_ALIGN_HISAT2"
+    script "../main.nf"
+    workflow "FASTQ_ALIGN_HISAT2"
+    config "./nextflow.config"
+
+        setup {
+            run("HISAT2_EXTRACTSPLICESITES") {
+                script "../../../../modules/nf-core/hisat2/extractsplicesites/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [id: 'test'],
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+
+            run("HISAT2_EXTRACTSPLICESITES", alias: "HISAT2_EXTRACTSPLICESITES_STUB") {
+                script "../../../../modules/nf-core/hisat2/extractsplicesites/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [id: 'test'],
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+
+            run("HISAT2_BUILD") {
+                script "../../../../modules/nf-core/hisat2/build/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [id: 'test'],
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                    ])
+                    input[1] = Channel.of([
+                        [id: 'test'],
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                    ])
+                    input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                    """
+                }
+            }
+
+            run("HISAT2_BUILD", alias: "HISAT2_BUILD_STUB") {
+                script "../../../../modules/nf-core/hisat2/build/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [id: 'test'],
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                    ])
+                    input[1] = Channel.of([
+                        [id: 'test'],
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+                    ])
+                    input[2] = HISAT2_EXTRACTSPLICESITES_STUB.out.txt
+                    """
+                }
+            }
+        }
+
+    test("sarscov2 - bam - single_end") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                input[3] = Channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    file(workflow.out.bai[0][1]).name,
+                    file(workflow.out.bam[0][1]).name,
+                    file(workflow.out.orig_bam[0][1]).name,
+                    workflow.out.csi,
+                    workflow.out.fastq,
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.stats,
+                    workflow.out.summary,
+                    workflow.out.versions).match()}
+            )
+        }
+    }
+    test("sarscov2 - bam - paired_end") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = HISAT2_BUILD.out.index
+                input[2] = HISAT2_EXTRACTSPLICESITES.out.txt
+                input[3] = Channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    file(workflow.out.bai[0][1]).name,
+                    file(workflow.out.bam[0][1]).name,
+                    file(workflow.out.orig_bam[0][1]).name,
+                    workflow.out.csi,
+                    workflow.out.fastq,
+                    workflow.out.flagstat,
+                    workflow.out.idxstats,
+                    workflow.out.stats,
+                    workflow.out.summary,
+                    workflow.out.versions).match()}
+            )
+        }
+    }
+
+    test("sarscov2 - bam - single_end - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = HISAT2_BUILD_STUB.out.index
+                input[2] = HISAT2_EXTRACTSPLICESITES_STUB.out.txt
+                input[3] = Channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+    test("sarscov2 - bam - paired_end - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ])
+                input[1] = HISAT2_BUILD_STUB.out.index
+                input[2] = HISAT2_EXTRACTSPLICESITES_STUB.out.txt
+                input[3] = Channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap
new file mode 100644
index 000000000..408dabff0
--- /dev/null
+++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap
@@ -0,0 +1,456 @@
+{
+    "sarscov2 - bam - single_end": {
+        "content": [
+            "test.sorted.bam.bai",
+            "test.sorted.bam",
+            "test.bam",
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.flagstat:md5,6de3bfde9582ad2532033832091f5c46"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.idxstats:md5,2a5df85e0d90e55bb2b359f6e05d5fbb"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.stats:md5,845655ccfd1fd701b9f692f8db9508af"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.hisat2.summary.log:md5,7b8a9e61b7646da1089b041333c41a87"
+                ]
+            ],
+            [
+                "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6",
+                "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8",
+                "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741",
+                "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a",
+                "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1",
+                "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:36:06.813423"
+    },
+    "sarscov2 - bam - single_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6",
+                    "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8",
+                    "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741",
+                    "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a",
+                    "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1",
+                    "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "fastq": [
+                    
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "orig_bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6",
+                    "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8",
+                    "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741",
+                    "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a",
+                    "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1",
+                    "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:36:23.861012"
+    },
+    "sarscov2 - bam - paired_end": {
+        "content": [
+            "test.sorted.bam.bai",
+            "test.sorted.bam",
+            "test.bam",
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.flagstat:md5,2fa0d90162a1b655863796c2a6bd8f45"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.idxstats:md5,1adb27b52d4d64b826f48b59d61dcd4d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.stats:md5,603fa8c9e0e9eb3769498fc989a29250"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.hisat2.summary.log:md5,9839b31db795958cc4b70711a3414e9c"
+                ]
+            ],
+            [
+                "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6",
+                "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8",
+                "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741",
+                "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a",
+                "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1",
+                "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T12:36:25.071168"
+    },
+    "sarscov2 - bam - paired_end - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6",
+                    "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8",
+                    "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741",
+                    "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a",
+                    "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1",
+                    "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "fastq": [
+                    
+                ],
+                "flagstat": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "idxstats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "orig_bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6",
+                    "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8",
+                    "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741",
+                    "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a",
+                    "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1",
+                    "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T19:36:44.894976"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/nextflow.config b/subworkflows/nf-core/fastq_align_hisat2/tests/nextflow.config
new file mode 100644
index 000000000..d2a119b55
--- /dev/null
+++ b/subworkflows/nf-core/fastq_align_hisat2/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: SAMTOOLS_SORT {
+        ext.prefix = { "${meta.id}.sorted" }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
index 3dbb27eae..ab6cbb320 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
@@ -12,11 +12,27 @@ include { FASTP                 } from '../../../modules/nf-core/fastp/main'
 //
 import groovy.json.JsonSlurper
 
-def getFastpReadsAfterFiltering(json_file) {
+def getFastpReadsAfterFiltering(json_file, min_num_reads) {
+
+    if ( workflow.stubRun ) { return min_num_reads }
+
     def Map json = (Map) new JsonSlurper().parseText(json_file.text).get('summary')
     return json['after_filtering']['total_reads'].toLong()
 }
 
+def getFastpAdapterSequence(json_file){
+
+    if ( workflow.stubRun ) { return "" }
+
+    def Map json = (Map) new JsonSlurper().parseText(json_file.text)
+    try{
+        adapter = json['adapter_cutting']['read1_adapter_sequence']
+    } catch(Exception ex){
+        adapter = ""
+    }
+    return adapter
+}
+
 workflow FASTQ_FASTQC_UMITOOLS_FASTP {
     take:
     reads             // channel: [ val(meta), [ reads ] ]
@@ -25,7 +41,7 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP {
     skip_umi_extract  // boolean: true/false
     umi_discard_read  // integer: 0, 1 or 2
     skip_trimming     // boolean: true/false
-    adapter_fasta     //    file: adapter.fasta
+    adapter_fasta     // file: adapter.fasta
     save_trimmed_fail // boolean: true/false
     save_merged       // boolean: true/false
     min_trimmed_reads // integer: > 0
@@ -75,10 +91,13 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP {
     fastqc_trim_html  = Channel.empty()
     fastqc_trim_zip   = Channel.empty()
     trim_read_count   = Channel.empty()
+    adapter_seq       = Channel.empty()
+
     if (!skip_trimming) {
         FASTP (
             umi_reads,
             adapter_fasta,
+            false, // don't want to set discard_trimmed_pass, else there will be no reads output
             save_trimmed_fail,
             save_merged
         )
@@ -96,7 +115,7 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP {
             .out
             .reads
             .join(trim_json)
-            .map { meta, reads, json -> [ meta, reads, getFastpReadsAfterFiltering(json) ] }
+            .map { meta, reads, json -> [ meta, reads, getFastpReadsAfterFiltering(json, min_trimmed_reads.toLong()) ] }
             .set { ch_num_trimmed_reads }
 
         ch_num_trimmed_reads
@@ -108,6 +127,10 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP {
             .map { meta, reads, num_reads -> [ meta, num_reads ] }
             .set { trim_read_count }
 
+        trim_json
+            .map { meta, json -> [meta, getFastpAdapterSequence(json)] }
+            .set { adapter_seq }
+
         if (!skip_fastqc) {
             FASTQC_TRIM (
                 trim_reads
@@ -125,6 +148,7 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP {
     fastqc_raw_zip     // channel: [ val(meta), [ zip ] ]
 
     umi_log            // channel: [ val(meta), [ log ] ]
+    adapter_seq        // channel: [ val(meta), [ adapter_seq] ]
 
     trim_json          // channel: [ val(meta), [ json ] ]
     trim_html          // channel: [ val(meta), [ html ] ]
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml
index f76b40261..9308fe9ba 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml
@@ -43,7 +43,7 @@ input:
   - skip_trimming:
       type: boolean
       description: |
-        Allows to skip trimgalore execution
+        Allows to skip FastP execution
   - adapter_fasta:
       type: file
       description: |
@@ -69,9 +69,8 @@ output:
   - reads:
       type: file
       description: >
-        Extracted FASTQ files. |
-        For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
-          For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
+        Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
+        For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
       pattern: "*.{fastq.gz}"
   - fastqc_html:
       type: file
@@ -116,9 +115,15 @@ output:
       type: file
       description: FastQC report archive
       pattern: "*_{fastqc.zip}"
+  - adapter_seq:
+      type: string
+      description: |
+        Adapter Sequence found in read1
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@robsyme"
+maintainers:
+  - "@robsyme"
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
new file mode 100644
index 000000000..38685f1d0
--- /dev/null
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
@@ -0,0 +1,79 @@
+if (!(params.skip_fastqc || params.skip_qc)) {
+    if (params.trimmer == 'fastp') {
+        process {
+            withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
+                ext.args   = '--quiet'
+                ext.prefix = { "${meta.id}_raw" }
+                publishDir = [
+                    path: { "${params.outdir}/fastqc/raw" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+
+            withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
+                ext.args   = '--quiet'
+                ext.prefix = { "${meta.id}_trimmed" }
+                publishDir = [
+                    path: { "${params.outdir}/fastqc/trim" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+}
+
+if (!params.skip_trimming) {
+    if (params.trimmer == 'fastp') {
+        process {
+            withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
+                ext.args   = { params.extra_fastp_args ?: '' }
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.trimmer}" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*.{json,html}"
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.trimmer}/log" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*.log"
+                    ],
+                    [
+                        path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
+                        mode: params.publish_dir_mode,
+                        pattern: "*.fastq.gz",
+                        saveAs: { params.save_trimmed ? it : null }
+                    ]
+                ]
+            }
+        }
+    }
+}
+
+if (params.with_umi && !params.skip_umi_extract) {
+    process {
+        withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:UMITOOLS_EXTRACT' {
+            ext.args   = { [
+                    params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
+                    params.umitools_bc_pattern     ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
+                    params.umitools_bc_pattern2    ? "--bc-pattern2='${params.umitools_bc_pattern2}'" : '',
+                    params.umitools_umi_separator  ? "--umi-separator='${params.umitools_umi_separator}'" : ''
+            ].join(' ').trim() }
+            publishDir = [
+                [
+                    path: { "${params.outdir}/umitools" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.log"
+                ],
+                [
+                    path: { params.save_umi_intermeds ? "${params.outdir}/umitools" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz",
+                    saveAs: { params.save_umi_intermeds ? it : null }
+                ]
+            ]
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test
new file mode 100644
index 000000000..eb944b7d5
--- /dev/null
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test
@@ -0,0 +1,964 @@
+nextflow_workflow {
+
+    name "Test Workflow FASTQ_FASTQC_UMITOOLS_FASTP"
+    script "../main.nf"
+    workflow "FASTQ_FASTQC_UMITOOLS_FASTP"
+    config './nextflow.config'
+
+    test("sarscov2 paired-end [fastq]") {
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.fastqc_raw_html },
+                { assert workflow.out.fastqc_raw_zip },
+                { assert workflow.out.fastqc_trim_html },
+                { assert workflow.out.fastqc_trim_zip },
+                { assert workflow.out.trim_html },
+                { assert workflow.out.trim_log },
+                { assert snapshot(
+                        workflow.out.adapter_seq,
+                        workflow.out.reads,
+                        workflow.out.trim_json,
+                        workflow.out.trim_read_count,
+                        workflow.out.trim_reads_fail,
+                        workflow.out.trim_reads_merged,
+                        workflow.out.umi_log,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("skip_fastqc") {
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = true
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.trim_html },
+                { assert workflow.out.trim_log },
+                { assert !workflow.out.fastqc_raw_html },
+                { assert !workflow.out.fastqc_raw_zip },
+                { assert !workflow.out.fastqc_trim_html },
+                { assert !workflow.out.fastqc_trim_zip },
+                { assert snapshot(
+                        workflow.out.adapter_seq,
+                        workflow.out.reads,
+                        workflow.out.trim_json,
+                        workflow.out.trim_read_count,
+                        workflow.out.trim_reads_fail,
+                        workflow.out.trim_reads_merged,
+                        workflow.out.umi_log,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("with_umi") {
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = true
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.fastqc_raw_html },
+                { assert workflow.out.fastqc_raw_zip },
+                { assert workflow.out.fastqc_trim_html },
+                { assert workflow.out.fastqc_trim_zip },
+                { assert workflow.out.trim_html },
+                { assert workflow.out.trim_log },
+                { assert snapshot(
+                        workflow.out.adapter_seq,
+                        workflow.out.reads,
+                        workflow.out.trim_json,
+                        workflow.out.trim_read_count,
+                        workflow.out.trim_reads_fail,
+                        workflow.out.trim_reads_merged,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+
+    test("skip_umi_extract") {
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = true
+                skip_umi_extract  = true
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.fastqc_raw_html },
+                { assert workflow.out.fastqc_raw_zip },
+                { assert workflow.out.fastqc_trim_html },
+                { assert workflow.out.fastqc_trim_zip },
+                { assert workflow.out.trim_html },
+                { assert workflow.out.trim_log },
+                { assert snapshot(
+                        workflow.out.adapter_seq,
+                        workflow.out.reads,
+                        workflow.out.trim_json,
+                        workflow.out.trim_read_count,
+                        workflow.out.trim_reads_fail,
+                        workflow.out.trim_reads_merged,
+                        workflow.out.umi_log,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("umi_discard_read = 2") {
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = true
+                skip_umi_extract  = true
+                umi_discard_read  = 2
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.fastqc_raw_html },
+                { assert workflow.out.fastqc_raw_zip },
+                { assert workflow.out.fastqc_trim_html },
+                { assert workflow.out.fastqc_trim_zip },
+                { assert workflow.out.trim_html },
+                { assert workflow.out.trim_log },
+                { assert snapshot(
+                        workflow.out.adapter_seq,
+                        workflow.out.reads,
+                        workflow.out.trim_json,
+                        workflow.out.trim_read_count,
+                        workflow.out.trim_reads_fail,
+                        workflow.out.trim_reads_merged,
+                        workflow.out.umi_log,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("skip_trimming") {
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = true
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.fastqc_raw_html },
+                { assert workflow.out.fastqc_raw_zip },
+                { assert !workflow.out.fastqc_trim_html },
+                { assert !workflow.out.fastqc_trim_zip },
+                { assert !workflow.out.trim_html },
+                { assert !workflow.out.trim_log },
+                { assert snapshot(
+                        // If we skip trimming then input is output, so not snapshotting
+                        workflow.out.adapter_seq,
+                        workflow.out.reads.get(0).get(0), // Reads meta map
+                        workflow.out.trim_json,
+                        workflow.out.trim_read_count,
+                        workflow.out.trim_reads_fail,
+                        workflow.out.trim_reads_merged,
+                        workflow.out.umi_log,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("save_trimmed_fail") {
+
+        config './nextflow.save_trimmed.config'
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = true
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.fastqc_raw_html },
+                { assert workflow.out.fastqc_raw_zip },
+                { assert workflow.out.fastqc_trim_html },
+                { assert workflow.out.fastqc_trim_zip },
+                { assert workflow.out.trim_html },
+                { assert workflow.out.trim_log },
+                { assert snapshot(
+                        workflow.out.adapter_seq,
+                        workflow.out.reads,
+                        workflow.out.trim_json,
+                        workflow.out.trim_read_count,
+                        workflow.out.trim_reads_fail,
+                        workflow.out.trim_reads_merged,
+                        workflow.out.umi_log,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("save_merged") {
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = true
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.fastqc_raw_html },
+                { assert workflow.out.fastqc_raw_zip },
+                { assert workflow.out.fastqc_trim_html },
+                { assert workflow.out.fastqc_trim_zip },
+                { assert workflow.out.trim_html },
+                { assert workflow.out.trim_log },
+                { assert snapshot(
+                        workflow.out.adapter_seq,
+                        workflow.out.reads,
+                        workflow.out.trim_json,
+                        workflow.out.trim_read_count,
+                        workflow.out.trim_reads_fail,
+                        workflow.out.trim_reads_merged,
+                        workflow.out.umi_log,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("min_trimmed_reads = 26") {
+        // Subworkflow should stop after FASTP which trims down to 25 reads
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = true
+                min_trimmed_reads = 26
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.fastqc_raw_html },
+                { assert workflow.out.fastqc_raw_zip },
+                { assert workflow.out.fastqc_trim_html },
+                { assert workflow.out.fastqc_trim_zip },
+                { assert workflow.out.trim_html },
+                { assert workflow.out.trim_log },
+                { assert snapshot(
+                        workflow.out.adapter_seq,
+                        workflow.out.reads,
+                        workflow.out.trim_json,
+                        workflow.out.trim_read_count,
+                        workflow.out.trim_reads_fail,
+                        workflow.out.trim_reads_merged,
+                        workflow.out.umi_log,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [fastq] - stub") {
+
+        options '-stub'
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("skip_fastqc - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = true
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end: false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("with_umi - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = true
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+
+    test("skip_umi_extract - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = true
+                skip_umi_extract  = true
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("umi_discard_read = 2 - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = true
+                skip_umi_extract  = true
+                umi_discard_read  = 2
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("skip_trimming - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = true
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.adapter_seq,
+                    workflow.out.fastqc_raw_html,
+                    workflow.out.fastqc_raw_zip,
+                    workflow.out.fastqc_trim_html,
+                    workflow.out.fastqc_trim_zip,
+                    workflow.out.trim_html,
+                    workflow.out.trim_json,
+                    workflow.out.trim_log,
+                    workflow.out.trim_read_count,
+                    workflow.out.trim_reads_fail,
+                    workflow.out.trim_reads_merged,
+                    workflow.out.umi_log,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test("save_trimmed_fail - stub") {
+
+        options "-stub"
+
+        config './nextflow.save_trimmed.config'
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = true
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("save_merged - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = true
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("min_trimmed_reads = 26 - stub") {
+        // Subworkflow should stop after FASTP which trims down to 25 reads
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = true
+                min_trimmed_reads = 26
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap
new file mode 100644
index 000000000..e7d1f51ed
--- /dev/null
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap
@@ -0,0 +1,2407 @@
+{
+    "skip_fastqc": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "unspecified"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7",
+                        "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    198
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:56:01.933832"
+    },
+    "save_trimmed_fail": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "unspecified"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,6ff32a64c5188b9a9192be1398c262c7",
+                        "test_2.fastp.fastq.gz:md5,db0cb7c9977e94ac2b4b446ebd017a8a"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    162
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.paired.fail.fastq.gz:md5,409b687c734cedd7a1fec14d316e1366",
+                        "test_1.fail.fastq.gz:md5,4f273cf3159c13f79e8ffae12f5661f6",
+                        "test_2.fail.fastq.gz:md5,f97b9edefb5649aab661fbc9e71fc995"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:57:38.736"
+    },
+    "skip_umi_extract": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "unspecified"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7",
+                        "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    198
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:56:47.905105"
+    },
+    "umi_discard_read = 2": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "unspecified"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7",
+                        "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    198
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:57:05.436744"
+    },
+    "umi_discard_read = 2 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        1
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "13": [
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        ""
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    
+                ],
+                "9": [
+                    
+                ],
+                "adapter_seq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        ""
+                    ]
+                ],
+                "fastqc_raw_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_raw_zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_trim_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_trim_zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
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+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_trim_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_trim_zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "trim_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_read_count": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        1
+                    ]
+                ],
+                "trim_reads_fail": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.paired.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "trim_reads_merged": [
+                    
+                ],
+                "umi_log": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:59:51.615894"
+    },
+    "skip_umi_extract - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        1
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "13": [
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        ""
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    
+                ],
+                "9": [
+                    
+                ],
+                "adapter_seq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        ""
+                    ]
+                ],
+                "fastqc_raw_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_raw_zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_trim_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_trim_zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "trim_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_read_count": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        1
+                    ]
+                ],
+                "trim_reads_fail": [
+                    
+                ],
+                "trim_reads_merged": [
+                    
+                ],
+                "umi_log": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:59:12.592278"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.config
new file mode 100644
index 000000000..0174cae50
--- /dev/null
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.config
@@ -0,0 +1,11 @@
+process {
+
+    withName: UMITOOLS_EXTRACT {
+        ext.args = '--bc-pattern="NNNN" --bc-pattern2="NNNN"'
+    }
+
+    withName: UMICOLLAPSE {
+        ext.prefix = { "${meta.id}.dedup" }
+    }
+
+}
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.save_trimmed.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.save_trimmed.config
new file mode 100644
index 000000000..21207addd
--- /dev/null
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.save_trimmed.config
@@ -0,0 +1,6 @@
+process {
+    // Make filtering more aggressive to make more reads fail
+    withName: FASTP {
+        ext.args = "-e 30"
+    }
+}
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml
index e32e90f43..a7df97f77 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml
@@ -47,13 +47,14 @@ input:
       type: integer
       description: |
         Inputs with fewer than this reads will be filtered out of the "reads" output channel
-
 output:
   - reads:
       type: file
       description: >
-        Extracted FASTQ files. |
-        For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
+        Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
+
+
+
           For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
       pattern: "*.{fastq.gz}"
   - fastqc_html:
@@ -95,3 +96,6 @@ output:
 authors:
   - "@drpatelh"
   - "@KamilMaliszArdigen"
+maintainers:
+  - "@drpatelh"
+  - "@KamilMaliszArdigen"
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
new file mode 100644
index 000000000..46c7a72b6
--- /dev/null
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
@@ -0,0 +1,89 @@
+if (!(params.skip_fastqc || params.skip_qc)) {
+    if (params.trimmer == 'trimgalore') {
+        process {
+            withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
+                ext.args   = '--quiet'
+                ext.prefix = { "${meta.id}_raw" }
+                publishDir = [
+                    path: { "${params.outdir}/fastqc/raw" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
+}
+
+if (!params.skip_trimming) {
+    if (params.trimmer == 'trimgalore') {
+        process {
+            withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE' {
+                ext.args   = {
+                    // Function to convert argument strings into a map
+                    def argsToMap = { String args ->
+                        args.split("\\s(?=--)").collectEntries {
+                            def parts = it.trim().split(/\s+/, 2)
+                            [(parts.first()): parts.last()]
+                        }
+                    }
+
+                    // Initialize the map with preconfigured values
+                    def preset_args_map = argsToMap("""
+                    --fastqc_args '-t ${task.cpus}'
+                    """.trim())
+
+                    // Consolidate the extra arguments
+                    def final_args_map = preset_args_map + (params.extra_trimgalore_args ? argsToMap(params.extra_trimgalore_args) : [:])
+
+                    // Convert the map back to a list and then to a single string
+                    final_args_map.collect { key, value -> "${key} ${value}" }.join(' ').trim()
+                }
+                ext.prefix = { "${meta.id}_trimmed" }
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/fastqc/trim" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*.{html,zip}"
+                    ],
+                    [
+                        path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
+                        mode: params.publish_dir_mode,
+                        pattern: "*.fq.gz",
+                        saveAs: { params.save_trimmed ? it : null }
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.trimmer}" },
+                        mode: params.publish_dir_mode,
+                        pattern: "*.txt"
+                    ]
+                ]
+            }
+        }
+    }
+}
+
+if (params.with_umi && !params.skip_umi_extract) {
+    process {
+        withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT' {
+            ext.args   = { [
+                    params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
+                    params.umitools_bc_pattern     ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
+                    params.umitools_bc_pattern2    ? "--bc-pattern2='${params.umitools_bc_pattern2}'" : '',
+                    params.umitools_umi_separator  ? "--umi-separator='${params.umitools_umi_separator}'" : ''
+            ].join(' ').trim() }
+            publishDir = [
+                [
+                    path: { "${params.outdir}/umitools" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.log"
+                ],
+                [
+                    path: { params.save_umi_intermeds ? "${params.outdir}/umitools" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz",
+                    saveAs: { params.save_umi_intermeds ? it : null }
+                ]
+            ]
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test
new file mode 100644
index 000000000..3fffd234b
--- /dev/null
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test
@@ -0,0 +1,263 @@
+nextflow_workflow {
+
+    name "Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE"
+    script "../main.nf"
+    workflow "FASTQ_FASTQC_UMITOOLS_TRIMGALORE"
+    config './nextflow.config'
+
+    test("test single end read with UMI") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = false // skip_fastqc
+                input[2] = true  // with_umi
+                input[3] = false // skip_umi_extract
+                input[4] = false // skip_trimming
+                input[5] = 1     // umi_discard_read
+                input[6] = 1     // min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert path(workflow.out.fastqc_html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(
+                    workflow.out.reads,
+                    workflow.out.trim_read_count,
+                    workflow.out.trim_unpaired,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test("test paired end read with UMI") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = false // skip_fastqc
+                input[2] = true  // with_umi
+                input[3] = false // skip_umi_extract
+                input[4] = false // skip_trimming
+                input[5] = 1     // umi_discard_read
+                input[6] = 1     // min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.reads,
+                    workflow.out.trim_read_count,
+                    workflow.out.trim_unpaired,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+    test("test paired end read without UMI") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = false // skip_fastqc
+                input[2] = false // with_umi
+                input[3] = false // skip_umi_extract
+                input[4] = false // skip_trimming
+                input[5] = 1     // umi_discard_read
+                input[6] = 1     // min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.reads,
+                    workflow.out.trim_read_count,
+                    workflow.out.trim_unpaired,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test("test skip all steps") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = true // skip_fastqc
+                input[2] = true // with_umi
+                input[3] = true // skip_umi_extract
+                input[4] = true // skip_trimming
+                input[5] = 0    // umi_discard_read
+                input[6] = 1    // min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.trim_read_count,
+                    workflow.out.trim_unpaired,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test("test single end read with UMI - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = false // skip_fastqc
+                input[2] = true  // with_umi
+                input[3] = false // skip_umi_extract
+                input[4] = false // skip_trimming
+                input[5] = 1     // umi_discard_read
+                input[6] = 1     // min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("test paired end read with UMI - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = false // skip_fastqc
+                input[2] = true  // with_umi
+                input[3] = false // skip_umi_extract
+                input[4] = false // skip_trimming
+                input[5] = 1     // umi_discard_read
+                input[6] = 1     // min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+    test("test paired end read without UMI - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = false // skip_fastqc
+                input[2] = false // with_umi
+                input[3] = false // skip_umi_extract
+                input[4] = false // skip_trimming
+                input[5] = 1     // umi_discard_read
+                input[6] = 1     // min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("test skip all steps - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = true // skip_fastqc
+                input[2] = true // with_umi
+                input[3] = true // skip_umi_extract
+                input[4] = true // skip_trimming
+                input[5] = 0    // umi_discard_read
+                input[6] = 1    // min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success}
+                // No snapshot when skipping all as output is input
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap
new file mode 100644
index 000000000..b37a75c9b
--- /dev/null
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap
@@ -0,0 +1,524 @@
+{
+    "test paired end read with UMI - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        0
+                    ]
+                ],
+                "9": [
+                    "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150",
+                    "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
+                ],
+                "fastqc_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    
+                ],
+                "trim_html": [
+                    
+                ],
+                "trim_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_read_count": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        0
+                    ]
+                ],
+                "trim_unpaired": [
+                    
+                ],
+                "trim_zip": [
+                    
+                ],
+                "umi_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150",
+                    "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:06:34.919444"
+    },
+    "test paired end read without UMI - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        0
+                    ]
+                ],
+                "9": [
+                    "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
+                ],
+                "fastqc_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    
+                ],
+                "trim_html": [
+                    
+                ],
+                "trim_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "trim_read_count": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        0
+                    ]
+                ],
+                "trim_unpaired": [
+                    
+                ],
+                "trim_zip": [
+                    
+                ],
+                "umi_log": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:06:51.765414"
+    },
+    "test paired end read without UMI": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1_val_1.fq.gz:md5,566d44cca0d22c522d6cf0e50c7165dc",
+                        "test_2_val_2.fq.gz:md5,3c023e8e890b897821df3dc98f48c2b3"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    100.0
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150",
+                "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:05:37.366404"
+    },
+    "test single end read with UMI": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_trimmed.fq.gz:md5,faae784affdd7d84e2fa9da9e9425229"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    100.0
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150",
+                "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
+                "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:04:53.072227"
+    },
+    "test paired end read with UMI": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_trimmed.fq.gz:md5,9c58b78ac2c7b5ce9ca6b090eee1d39c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    100.0
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150",
+                "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
+                "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:05:16.709704"
+    },
+    "test skip all steps": {
+        "content": [
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:05:49.455992"
+    },
+    "test single end read with UMI - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        0
+                    ]
+                ],
+                "9": [
+                    "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150",
+                    "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
+                ],
+                "fastqc_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    
+                ],
+                "trim_html": [
+                    
+                ],
+                "trim_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_read_count": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        0
+                    ]
+                ],
+                "trim_unpaired": [
+                    
+                ],
+                "trim_zip": [
+                    
+                ],
+                "umi_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150",
+                    "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839",
+                    "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T17:06:09.844235"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/nextflow.config
new file mode 100644
index 000000000..06a7d07a7
--- /dev/null
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: UMITOOLS_EXTRACT {
+        ext.args = '--bc-pattern="NNNN"'
+    }
+}
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
new file mode 100644
index 000000000..4c7b25f8e
--- /dev/null
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
@@ -0,0 +1,319 @@
+import groovy.json.JsonSlurper
+
+include { BBMAP_BBSPLIT                   } from '../../../modules/nf-core/bbmap/bbsplit'
+include { CAT_FASTQ                       } from '../../../modules/nf-core/cat/fastq/main'
+include { SORTMERNA                       } from '../../../modules/nf-core/sortmerna/main'
+include { SORTMERNA as SORTMERNA_INDEX    } from '../../../modules/nf-core/sortmerna/main'
+
+include { FASTQ_SUBSAMPLE_FQ_SALMON        } from '../fastq_subsample_fq_salmon'
+include { FASTQ_FASTQC_UMITOOLS_TRIMGALORE } from '../fastq_fastqc_umitools_trimgalore'
+include { FASTQ_FASTQC_UMITOOLS_FASTP      } from '../fastq_fastqc_umitools_fastp'
+
+def pass_trimmed_reads = [:]
+
+//
+// Function to determine library type by comparing type counts.
+//
+
+//
+def calculateStrandedness(forwardFragments, reverseFragments, unstrandedFragments, stranded_threshold=0.8, unstranded_threshold=0.1) {
+    def totalFragments = forwardFragments + reverseFragments + unstrandedFragments
+    def totalStrandedFragments = forwardFragments + reverseFragments
+
+    def library_strandedness = 'undetermined'
+    if (totalStrandedFragments > 0) {
+        def forwardProportion = forwardFragments / (totalStrandedFragments as double)
+        def reverseProportion = reverseFragments / (totalStrandedFragments as double)
+        def proportionDifference = Math.abs(forwardProportion - reverseProportion)
+
+        if (forwardProportion >= stranded_threshold) {
+            strandedness = 'forward'
+        } else if (reverseProportion >= stranded_threshold) {
+            strandedness = 'reverse'
+        } else if (proportionDifference <= unstranded_threshold) {
+            strandedness = 'unstranded'
+        }
+    }
+
+    return [
+        inferred_strandedness: strandedness,
+        forwardFragments: (forwardFragments / (totalFragments as double)) * 100,
+        reverseFragments: (reverseFragments / (totalFragments as double)) * 100,
+        unstrandedFragments: (unstrandedFragments / (totalFragments as double)) * 100
+    ]
+}
+
+//
+// Function that parses Salmon quant 'lib_format_counts.json' output file to get inferred strandedness
+//
+def getSalmonInferredStrandedness(json_file, stranded_threshold = 0.8, unstranded_threshold = 0.1) {
+    // Parse the JSON content of the file
+    def libCounts = new JsonSlurper().parseText(json_file.text)
+
+    // Calculate the counts for forward and reverse strand fragments
+    def forwardKeys = ['SF', 'ISF', 'MSF', 'OSF']
+    def reverseKeys = ['SR', 'ISR', 'MSR', 'OSR']
+
+    // Calculate unstranded fragments (IU and U)
+    // NOTE: this is here for completeness, but actually all fragments have a
+    // strandedness (even if the overall library does not), so all these values
+    // will be '0'. See
+    // https://groups.google.com/g/sailfish-users/c/yxzBDv6NB6I
+    def unstrandedKeys = ['IU', 'U', 'MU']
+
+    def forwardFragments = forwardKeys.collect { libCounts[it] ?: 0 }.sum()
+    def reverseFragments = reverseKeys.collect { libCounts[it] ?: 0 }.sum()
+    def unstrandedFragments = unstrandedKeys.collect { libCounts[it] ?: 0 }.sum()
+
+    // Use shared calculation function to determine strandedness
+    return calculateStrandedness(forwardFragments, reverseFragments, unstrandedFragments, stranded_threshold, unstranded_threshold)
+}
+
+//
+// Create MultiQC tsv custom content from a list of values
+//
+def multiqcTsvFromList(tsv_data, header) {
+    def tsv_string = ""
+    if (tsv_data.size() > 0) {
+        tsv_string += "${header.join('\t')}\n"
+        tsv_string += tsv_data.join('\n')
+    }
+    return tsv_string
+}
+
+workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
+
+    take:
+    ch_reads             // channel: [ val(meta), [ reads ] ]
+    ch_fasta             // channel: /path/to/genome.fasta
+    ch_transcript_fasta  // channel: /path/to/transcript.fasta
+    ch_gtf               // channel: /path/to/genome.gtf
+    ch_salmon_index      // channel: /path/to/salmon/index/ (optional)
+    ch_sortmerna_index   // channel: /path/to/sortmerna/index/ (optional)
+    ch_bbsplit_index     // channel: /path/to/bbsplit/index/ (optional)
+    ch_rrna_fastas       // channel: one or more fasta files containing rrna sequences to be passed to SortMeRNA (optional)
+    skip_bbsplit         // boolean: Skip BBSplit for removal of non-reference genome reads.
+    skip_fastqc          // boolean: true/false
+    skip_trimming        // boolean: true/false
+    skip_umi_extract     // boolean: true/false
+    make_salmon_index    // boolean: Whether to create salmon index before running salmon quant
+    make_sortmerna_index // boolean: Whether to create a sortmerna index before running sortmerna
+    trimmer              // string (enum): 'fastp' or 'trimgalore'
+    min_trimmed_reads    // integer: > 0
+    save_trimmed         // boolean: true/false
+    remove_ribo_rna      // boolean: true/false: whether to run sortmerna to remove rrnas
+    with_umi             // boolean: true/false: Enable UMI-based read deduplication.
+    umi_discard_read     // integer: 0, 1 or 2
+    stranded_threshold   // float: The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5
+    unstranded_threshold // float: The difference in fraction of stranded reads assigned to 'forward' and 'reverse' below which a sample is classified as 'unstranded'
+
+    main:
+
+    ch_versions        = Channel.empty()
+    ch_filtered_reads  = Channel.empty()
+    ch_trim_read_count = Channel.empty()
+    ch_multiqc_files   = Channel.empty()
+
+    ch_reads
+        .branch {
+            meta, fastqs ->
+                single  : fastqs.size() == 1
+                    return [ meta, fastqs.flatten() ]
+                multiple: fastqs.size() > 1
+                    return [ meta, fastqs.flatten() ]
+        }
+        .set { ch_fastq }
+
+    //
+    // MODULE: Concatenate FastQ files from same sample if required
+    //
+    CAT_FASTQ (
+        ch_fastq.multiple
+    )
+    .reads
+    .mix(ch_fastq.single)
+    .set { ch_filtered_reads }
+
+    ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first())
+
+    //
+    // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore!
+    //
+    if (trimmer == 'trimgalore') {
+        FASTQ_FASTQC_UMITOOLS_TRIMGALORE (
+            ch_filtered_reads,
+            skip_fastqc,
+            with_umi,
+            skip_umi_extract,
+            skip_trimming,
+            umi_discard_read,
+            min_trimmed_reads
+        )
+        ch_filtered_reads      = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.reads
+        ch_trim_read_count     = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_read_count
+
+        ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.versions)
+        ch_multiqc_files = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.fastqc_zip
+            .mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_zip)
+            .mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log)
+            .mix(ch_multiqc_files)
+    }
+
+    //
+    // SUBWORKFLOW: Read QC, extract UMI and trim adapters with fastp
+    //
+    if (trimmer == 'fastp') {
+        FASTQ_FASTQC_UMITOOLS_FASTP (
+            ch_filtered_reads,
+            skip_fastqc,
+            with_umi,
+            skip_umi_extract,
+            umi_discard_read,
+            skip_trimming,
+            [],
+            save_trimmed,
+            save_trimmed,
+            min_trimmed_reads
+        )
+        ch_filtered_reads      = FASTQ_FASTQC_UMITOOLS_FASTP.out.reads
+        ch_trim_read_count     = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_read_count
+
+        ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.versions)
+        ch_multiqc_files = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip
+            .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip)
+            .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json.map{tuple(it[0], [it[1]])})
+            .mix(ch_multiqc_files)
+    }
+
+    //
+    // Get list of samples that failed trimming threshold for MultiQC report
+    //
+
+    ch_trim_read_count
+        .map {
+            meta, num_reads ->
+                pass_trimmed_reads[meta.id] = true
+                if (num_reads <= min_trimmed_reads.toFloat()) {
+                    pass_trimmed_reads[meta.id] = false
+                    return [ "$meta.id\t$num_reads" ]
+                }
+        }
+        .collect()
+        .map {
+            tsv_data ->
+                def header = ["Sample", "Reads after trimming"]
+                multiqcTsvFromList(tsv_data, header)
+        }
+        .set { ch_fail_trimming_multiqc }
+
+    ch_multiqc_files = ch_multiqc_files
+        .mix(
+            ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv')
+        )
+
+    //
+    // MODULE: Remove genome contaminant reads
+    //
+    if (!skip_bbsplit) {
+        BBMAP_BBSPLIT (
+            ch_filtered_reads,
+            ch_bbsplit_index,
+            [],
+            [ [], [] ],
+            false
+        )
+
+        BBMAP_BBSPLIT.out.primary_fastq
+            .set { ch_filtered_reads }
+
+        ch_versions = ch_versions.mix(BBMAP_BBSPLIT.out.versions.first())
+    }
+
+    //
+    // MODULE: Remove ribosomal RNA reads
+    //
+    if (remove_ribo_rna) {
+        ch_sortmerna_fastas = ch_rrna_fastas
+            .collect()
+            .map{ ['rrna_refs', it] }
+
+        if (make_sortmerna_index) {
+            SORTMERNA_INDEX (
+                [[],[]],
+                ch_sortmerna_fastas,
+                [[],[]]
+            )
+            ch_sortmerna_index = SORTMERNA_INDEX.out.index.first()
+        }
+
+        SORTMERNA (
+            ch_filtered_reads,
+            ch_sortmerna_fastas,
+            ch_sortmerna_index
+        )
+
+        SORTMERNA.out.reads
+            .set { ch_filtered_reads }
+
+        ch_multiqc_files = ch_multiqc_files
+            .mix(SORTMERNA.out.log)
+
+        ch_versions = ch_versions.mix(SORTMERNA.out.versions.first())
+    }
+
+    // Branch FastQ channels if 'auto' specified to infer strandedness
+    ch_filtered_reads
+        .branch {
+            meta, fastq ->
+                auto_strand : meta.strandedness == 'auto'
+                    return [ meta, fastq ]
+                known_strand: meta.strandedness != 'auto'
+                    return [ meta, fastq ]
+        }
+        .set { ch_strand_fastq }
+
+    //
+    // SUBWORKFLOW: Sub-sample FastQ files and pseudoalign with Salmon to auto-infer strandedness
+    //
+    // Return empty channel if ch_strand_fastq.auto_strand is empty so salmon index isn't created
+
+    ch_fasta
+        .combine(ch_strand_fastq.auto_strand)
+        .map { it.first() }
+        .first()
+        .set { ch_genome_fasta }
+
+    FASTQ_SUBSAMPLE_FQ_SALMON (
+        ch_strand_fastq.auto_strand,
+        ch_genome_fasta,
+        ch_transcript_fasta,
+        ch_gtf,
+        ch_salmon_index,
+        make_salmon_index
+    )
+    ch_versions = ch_versions.mix(FASTQ_SUBSAMPLE_FQ_SALMON.out.versions)
+
+    FASTQ_SUBSAMPLE_FQ_SALMON
+        .out
+        .lib_format_counts
+        .join(ch_strand_fastq.auto_strand)
+        .map {
+            meta, json, reads ->
+                def salmon_strand_analysis = getSalmonInferredStrandedness(json, stranded_threshold=stranded_threshold, unstranded_threshold=unstranded_threshold)
+                strandedness = salmon_strand_analysis.inferred_strandedness
+                if (strandedness == 'undetermined') {
+                    strandedness = 'unstranded'
+                }
+                return [ meta + [ strandedness: strandedness, salmon_strand_analysis: salmon_strand_analysis ], reads ]
+        }
+        .mix(ch_strand_fastq.known_strand)
+        .set { ch_strand_inferred_fastq }
+
+    emit:
+
+    reads           = ch_strand_inferred_fastq
+    trim_read_count = ch_trim_read_count
+
+    multiqc_files   = ch_multiqc_files.transpose().map{it[1]}
+    versions        = ch_versions                     // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml
new file mode 100644
index 000000000..6f92f56a0
--- /dev/null
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml
@@ -0,0 +1,132 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "fastq_qc_trim_filter_setstrandedness"
+description: Basic FASTQ preprocessing for RNA-seq
+keywords:
+  - fastq
+  - rnaseq
+  - rrna
+  - trimming
+  - subsample
+  - strandedness
+components:
+  - bbmap/bbsplit
+  - samtools/sort
+  - samtools/index
+  - cat
+  - cat/fastq
+  - sortmerna
+  - fastq_subsample_fq_salmon
+  - fastq_fastqc_umitools_trimgalore
+  - fastq_fastqc_umitools_fastp
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - ch_reads:
+      type: file
+      description: |
+        Channel with input FastQ files of size 1 and 2 for single-end and
+        paired-end data, respectively.
+  - ch_fasta:
+      type: file
+      description: Channel with genome sequence in fasta format
+  - ch_transcript_fasta:
+      type: file
+      description: Channel with transcriptome sequence in fasta format
+  - ch_gtf:
+      type: file
+      description: Channel with features in GTF format
+  - ch_salmon_index:
+      type: file
+      description: Directory containing Salmon index
+  - ch_sortmerna_index:
+      type: file
+      description: Directory containing sortmerna index
+  - ch_bbsplit_index:
+      type: file
+      description: Path to directory or tar.gz archive for pre-built BBSplit index
+  - ch_rrna_fastas:
+      type: file
+      description: |
+        Channel containing one or more FASTA files containing rRNA sequences
+        for use with SortMeRNA
+  - skip_bbsplit:
+      type: boolean
+      description: Whether to skip BBSplit for removal of non-reference genome reads
+  - skip_fastqc:
+      type: boolean
+      description: Whether to skip FastQC
+  - skip_trimming:
+      type: boolean
+      description: Whether to skip trimming
+  - skip_umi_extract:
+      type: boolean
+      description: |
+        Skip the UMI extraction from the read in case the UMIs have been moved
+        to the headers in advance of the pipeline run
+  - make_salmon_index:
+      type: boolean
+      description: Whether to create salmon index before running salmon quant
+  - make_sortmerna_index:
+      type: boolean
+      description: Whether to create sortmerna index before running sortmerna
+  - trimmer:
+      type: string
+      description: |
+        Specifies the trimming tool to use - available options are 'trimgalore'
+        and 'fastp'
+  - min_trimmed_reads:
+      type: integer
+      description: |
+        Minimum number of trimmed reads below which samples are removed from
+        further processing
+  - save_trimmed:
+      type: boolean
+      description: Save the trimmed FastQ files in the results directory?
+  - remove_ribo_rna:
+      type: boolean
+      description: Enable the removal of reads derived from ribosomal RNA using SortMeRNA?
+  - with_umi:
+      type: boolean
+      description: Enable UMI-based read deduplication
+  - umi_discard_read:
+      type: integer
+      description: |
+        After UMI barcode extraction discard either R1 or R2 by setting this
+        parameter to 1 or 2, respectively
+  - stranded_threshold:
+      type: float
+      min: 0.5
+      description: |
+        The fraction of stranded reads that must be assigned to a strandedness
+        for confident assignment. Must be at least 0.5.
+  - unstranded_threshold:
+      type: float
+      description: |
+        The difference in fraction of stranded reads assigned to 'forward' and
+        'reverse' below which a sample is classified as 'unstranded'.
+
+output:
+  - reads:
+      type: file
+      description: Preprocessed fastq reads
+      pattern: "*.{fq,fastq}{,.gz}"
+  - multiqc_files:
+      type: file
+      description: MultiQC-compatible output files from tools used in prepreocessing
+      pattern: "*"
+  - trim_read_count:
+      type: integer
+      description: Number of reads remaining after trimming for all input samples
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@pinin4fjords"
+maintainers:
+  - "@pinin4fjords"
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.function.nf.test b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.function.nf.test
new file mode 100644
index 000000000..57fcd302b
--- /dev/null
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.function.nf.test
@@ -0,0 +1,118 @@
+nextflow_function {
+
+    name "Test Functions"
+    script "../main.nf"
+    
+    //
+    // Test function for deriving strandedness from Salmon numbers
+    //
+
+    test("Test Function getSalmonInferredStrandedness unstranded") {
+
+        function "getSalmonInferredStrandedness"
+
+        when {
+            function {
+                """
+                import groovy.json.JsonOutput
+
+                // Define the JSON contents for the test
+                def json_contents = JsonOutput.toJson([
+                    "SF": 0,
+                    "SR": 0,
+                    "ISF": 100,
+                    "ISR": 100,
+                    "IU": 0,
+                    "U": 0
+                ])
+                def jsonFile = file("${workDir}/salmonUnstranded.json")
+                jsonFile.write(json_contents)
+
+                input[0] = jsonFile
+                input[1] = 0.8
+                input[2] = 0.1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function getSalmonInferredStrandedness forward") {
+
+        function "getSalmonInferredStrandedness"
+
+        when {
+            function {
+                """
+                import groovy.json.JsonOutput
+
+                def json_contents = JsonOutput.toJson([
+                    "SF": 0,
+                    "SR": 0,
+                    "ISF": 100,
+                    "ISR": 0,
+                    "IU": 0,
+                    "U": 0
+                ])
+                def jsonFile = file("${workDir}/salmonForward.json")
+                jsonFile.write(json_contents)
+
+                input[0] = jsonFile
+                input[1] = 0.8
+                input[2] = 0.1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function getSalmonInferredStrandedness reverse") {
+
+        function "getSalmonInferredStrandedness"
+
+        when {
+            function {
+                """
+                import groovy.json.JsonOutput
+
+                def json_contents = JsonOutput.toJson([
+                    "SF": 0,
+                    "SR": 0,
+                    "ISF": 0,
+                    "ISR": 100,
+                    "IU": 0,
+                    "U": 0
+                ])
+                def jsonFile = file("${workDir}/salmonReverse.json")
+                jsonFile.write(json_contents)
+
+                input[0] = jsonFile
+                input[1] = 0.8
+                input[2] = 0.1
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+}
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.function.nf.test.snap b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.function.nf.test.snap
new file mode 100644
index 000000000..4b4e2e874
--- /dev/null
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.function.nf.test.snap
@@ -0,0 +1,47 @@
+{
+    "Test Function getSalmonInferredStrandedness forward": {
+        "content": [
+            {
+                "inferred_strandedness": "forward",
+                "forwardFragments": 100.0,
+                "reverseFragments": 0.0,
+                "unstrandedFragments": 0.0
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:28:59.284820592"
+    },
+    "Test Function getSalmonInferredStrandedness unstranded": {
+        "content": [
+            {
+                "inferred_strandedness": "unstranded",
+                "forwardFragments": 50.0,
+                "reverseFragments": 50.0,
+                "unstrandedFragments": 0.0
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:28:47.514036696"
+    },
+    "Test Function getSalmonInferredStrandedness reverse": {
+        "content": [
+            {
+                "inferred_strandedness": "reverse",
+                "forwardFragments": 0.0,
+                "reverseFragments": 100.0,
+                "unstrandedFragments": 0.0
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:29:11.43961965"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test
new file mode 100644
index 000000000..c752e176c
--- /dev/null
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test
@@ -0,0 +1,120 @@
+nextflow_workflow {
+
+    name "Test Subworkflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS"
+    script "../main.nf"
+    workflow "FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS"
+    config "./nextflow.config"
+
+    test("homo_sapiens paired-end [fastq] fastp") {
+
+        when {
+            workflow {
+                """
+                ch_reads = Channel.of([
+                    [ id:'test', single_end:false, strandedness:'auto' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+
+                input[0] = ch_reads
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) // ch_fasta
+                input[2] = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)) // ch_transcript_fasta
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)) // ch_gtf
+                input[4] = []              // ch_salmon_index
+                input[5] = []              // ch_sortmerna_index
+                input[6] = []              // ch_bbsplit_index
+                input[7] = Channel.of(file('https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5.8s-database-id98.fasta', checkIfExists: true)) // ch_rrna_fastas 
+                input[8] = true            // skip_bbsplit
+                input[9] = false           // skip_fastqc
+                input[10] = false           // skip_trimming
+                input[11] = true           // skip_umi_extract
+                input[12] = true           // make_salmon_index
+                input[13] = true           // make_sortmerna_index
+                input[14] = 'fastp'        // trimmer
+                input[15] = 10             // min_trimmed_reads
+                input[16] = true           // save_trimmed
+                input[17] = true           // remove_ribo_rna
+                input[18] = false          // with_umi
+                input[19] = 0              // umi_discard_read
+                input[20] = 0.8            // stranded_threshold
+                input[21] = 0.1            // unstranded_threshold
+                """
+            }
+        }
+
+        then {
+            def pelines1 = path(workflow.out.reads[0][1][0]).linesGzip
+            def pelines2 = path(workflow.out.reads[0][1][1]).linesGzip
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(pelines1).md5().match("fastp_test_pe_reads_1_lines") },
+                { assert snapshot(pelines1.size()).match("fastp_test_pe_reads_1_size") },
+                { assert snapshot(pelines2).md5().match("fastp_test_pe_reads_2_lines") },
+                { assert snapshot(pelines2.size()).match("fastp_test_pe_reads_2_size") },
+                { assert snapshot(workflow.out.trim_read_count).match("fastp_read_count") }
+                // This doesn't work- 'cat' changes between Conda and Docker -
+                // leaving it here until we find a way to address that
+                // { assert snapshot(workflow.out.versions).match("fastp_versions") }
+            )
+        }
+    }
+    test("homo_sapiens paired-end [fastq] trimgalore") {
+
+        when {
+            workflow {
+                """
+                ch_reads = Channel.of([
+                    [ id:'test', single_end:false, strandedness:'auto' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+
+                input[0] = ch_reads
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) // ch_fasta
+                input[2] = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)) // ch_transcript_fasta
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)) // ch_gtf
+                input[4] = []              // ch_salmon_index
+                input[5] = []              // ch_sortmerna_index
+                input[6] = []              // ch_bbsplit_index
+                input[7] = Channel.of(file('https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5.8s-database-id98.fasta', checkIfExists: true)) // ch_rrna_fastas 
+                input[8] = true            // skip_bbsplit
+                input[9] = false           // skip_fastqc
+                input[10] = false           // skip_trimming
+                input[11] = true           // skip_umi_extract
+                input[12] = true           // make_salmon_index
+                input[13] = true           // make_sortmerna_index
+                input[14] = 'fastp'        // trimmer
+                input[15] = 10             // min_trimmed_reads
+                input[16] = true           // save_trimmed
+                input[17] = true           // remove_ribo_rna
+                input[18] = false          // with_umi
+                input[19] = 0              // umi_discard_read
+                input[20] = 0.8            // stranded_threshold
+                input[21] = 0.1            // unstranded_threshold
+                """
+            }
+        }
+
+        then {
+            def pelines1 = path(workflow.out.reads[0][1][0]).linesGzip
+            def pelines2 = path(workflow.out.reads[0][1][1]).linesGzip
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(pelines1).md5().match("trimgalore_test_pe_reads_1_lines") },
+                { assert snapshot(pelines1.size()).match("trimgalore_test_pe_reads_1_size") },
+                { assert snapshot(pelines2).md5().match("trimgalore_test_pe_reads_2_lines") },
+                { assert snapshot(pelines2.size()).match("trimgalore_test_pe_reads_2_size") },
+                { assert snapshot(workflow.out.trim_read_count).match("trimgalore_read_count") }
+                // This doesn't work- 'cat' changes between Conda and Docker -
+                // leaving it here until we find a way to address that
+                //{ assert snapshot(workflow.out.versions).match("trimgalore_versions") }
+            )
+        }
+    }
+    
+
+}
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test.snap
new file mode 100644
index 000000000..985349317
--- /dev/null
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test.snap
@@ -0,0 +1,112 @@
+{
+    "fastp_read_count": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "strandedness": "auto"
+                    },
+                    3022
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:24:00.044553245"
+    },
+    "trimgalore_test_pe_reads_2_lines": {
+        "content": "eccf3e9e74589ff01c77fce7f4548e41",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:24:26.838793051"
+    },
+    "fastp_test_pe_reads_1_size": {
+        "content": [
+            4508
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:23:59.889337984"
+    },
+    "trimgalore_test_pe_reads_1_size": {
+        "content": [
+            4508
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:24:26.778599725"
+    },
+    "trimgalore_test_pe_reads_1_lines": {
+        "content": "3868fc1caf09367141d2bbf47e158823",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:24:26.774975135"
+    },
+    "fastp_test_pe_reads_2_lines": {
+        "content": "eccf3e9e74589ff01c77fce7f4548e41",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:23:59.997625278"
+    },
+    "fastp_test_pe_reads_2_size": {
+        "content": [
+            4508
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:24:00.042449965"
+    },
+    "trimgalore_test_pe_reads_2_size": {
+        "content": [
+            4508
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:24:26.841434261"
+    },
+    "fastp_test_pe_reads_1_lines": {
+        "content": "3868fc1caf09367141d2bbf47e158823",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:23:59.882844295"
+    },
+    "trimgalore_read_count": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false,
+                        "strandedness": "auto"
+                    },
+                    3022
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T10:24:26.84402498"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/nextflow.config b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/nextflow.config
new file mode 100644
index 000000000..9e33e4b33
--- /dev/null
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/nextflow.config
@@ -0,0 +1,27 @@
+//
+// Read subsampling and strand inferring options
+//
+
+process {
+    withName: 'FQ_SUBSAMPLE' {
+        ext.args   = '--record-count 1000000 --seed 1'
+        ext.prefix = { "${meta.id}.subsampled" }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
+        ext.args   = '--skipQuant --minAssignedFrags 1'
+        publishDir = [
+            enabled: false
+        ]
+    }
+    withName: 'SORTMERNA' {
+        ext.args  = '--index 0'
+    }
+    withName: 'SORTMERNA_INDEX' {
+        ext.args  = '--index 1'
+    }
+}
+
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf b/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf
index 0ac3e53a3..bac581cfa 100644
--- a/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf
@@ -43,12 +43,13 @@ workflow FASTQ_SUBSAMPLE_FQ_SALMON {
     ch_versions = ch_versions.mix(SALMON_QUANT.out.versions.first())
 
     emit:
-    index     = ch_index                   // channel: [ index ]
+    index             = ch_index                           // channel: [ index ]
 
-    reads     = FQ_SUBSAMPLE.out.fastq     // channel: [ val(meta), fastq ]
+    reads             = FQ_SUBSAMPLE.out.fastq             // channel: [ val(meta), fastq ]
 
-    results   = SALMON_QUANT.out.results   // channel: [ val(meta), results_dir ]
-    json_info = SALMON_QUANT.out.json_info // channel: [ val(meta), json_info
+    results           = SALMON_QUANT.out.results           // channel: [ val(meta), results_dir ]
+    json_info         = SALMON_QUANT.out.json_info         // channel: [ val(meta), json_info
+    lib_format_counts = SALMON_QUANT.out.lib_format_counts // channel: [ val(meta), json_info
 
-    versions  = ch_versions                // channel: [ versions.yml ]
+    versions          = ch_versions                        // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml b/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml
index d144269ba..7e2f10966 100644
--- a/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml
@@ -39,7 +39,6 @@ input:
   - make_index:
       type: boolean
       description: Whether to create salmon index before running salmon quant
-
 output:
   - index:
       type: directory
@@ -66,3 +65,6 @@ output:
 authors:
   - "@robsyme"
   - "@drpatelh"
+maintainers:
+  - "@robsyme"
+  - "@drpatelh"
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config b/subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config
new file mode 100644
index 000000000..36a8c5d7a
--- /dev/null
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config
@@ -0,0 +1,16 @@
+process {
+    withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE' {
+        ext.args   = '--record-count 1000000 --seed 1'
+        ext.prefix = { "${meta.id}.subsampled" }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
+        ext.args   = '--skipQuant'
+        publishDir = [
+            enabled: false
+        ]
+    }
+}
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test
new file mode 100644
index 000000000..077d9c758
--- /dev/null
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test
@@ -0,0 +1,104 @@
+nextflow_workflow {
+
+    name "Test Workflow FASTQ_SUBSAMPLE_FQ_SALMON"
+    script "../main.nf"
+    workflow "FASTQ_SUBSAMPLE_FQ_SALMON"
+    config "./nextflow.config"
+
+    test("homo_sapiens paired-end [fastq]") {
+
+        setup {
+            run("SALMON_INDEX") {
+                script "../../../../modules/nf-core/salmon/index/main.nf"
+                process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))        // genome_fasta
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true)) // transcriptome_fasta
+                """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                make_index = false
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))        // genome_fasta
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true)) // transcriptome_fasta
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true))          // genome_gtf
+                input[4] = SALMON_INDEX.out.index
+                input[5] = make_index
+                """
+            }
+        }
+
+        then {
+            def readlines1 = path(workflow.out.reads[0][1][0]).linesGzip
+            def readlines2 = path(workflow.out.reads[0][1][1]).linesGzip
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.index },
+                { assert workflow.out.json_info },
+                { assert workflow.out.results },
+                { assert snapshot(
+                    readlines1[0..5],
+                    readlines1.size(),
+                    readlines2[0..5],
+                    readlines2.size(),
+                    workflow.out.lib_format_counts,
+                    workflow.out.versions).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens paired-end [fastq] - stub") {
+
+        options "-stub"
+
+        setup {
+            run("SALMON_INDEX") {
+                script "../../../../modules/nf-core/salmon/index/main.nf"
+                process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))        // genome_fasta
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true)) // transcriptome_fasta
+                """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                make_index = false
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))        // genome_fasta
+                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true)) // transcriptome_fasta
+                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true))          // genome_gtf
+                input[4] = SALMON_INDEX.out.index
+                input[5] = make_index
+                """
+            }
+        }
+
+        then {
+            def readlines1 = path(workflow.out.reads[0][1][0]).linesGzip
+            def readlines2 = path(workflow.out.reads[0][1][1]).linesGzip
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap
new file mode 100644
index 000000000..e0c944f31
--- /dev/null
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap
@@ -0,0 +1,181 @@
+{
+    "homo_sapiens paired-end [fastq]": {
+        "content": [
+            [
+                "@normal#21#998579#1/1",
+                "CCTTCTCCCTGCTGGGGTTGCTTGTCAGTAGCGGGCAAGGTAGGAGTGTGGCGCTTTATTGCATTTACTTTCCCTCCCCCTTCCCCCCGGCCAAGAGAGG",
+                "+",
+                "102302000331;3333;23133320233330*33/233333333333333/313232333/3;3;3/333000;11/00;;01//103*1032323233",
+                "@normal#21#998572#2/1",
+                "CTCCTCTCCTTCTACCTGCTGGGGTTGCTTGTCAGTAGCGGGCAAGGTCGGAGTGTTGCGCTTTATTGCATTTACTTTCCCTCCCCCTTCCACCCGGCCA"
+            ],
+            1066944,
+            [
+                "@normal#21#998579#1/2",
+                "AAAAAAAAAGAAGAAGCAGAAGCTGTTTCCCTGGATATCCTGCTCACCGATTCCCCTCTCCAATTCTGTATTTTCCCTTCTCTTATTTAAGGGTCTCCAC",
+                "+",
+                "023333233332333310333302333211/3333;0300;*/;000/32;201003031/22;21333032;;11/23030322;2332333313/030",
+                "@normal#21#998572#2/2",
+                "TTCCCCTCTCCAATTGAGTATTTTCCCTTCTCTTATTTAAGGGTCTCCACACAAACAGATACAATTTTAGGGACAGCTAGGAGAAAGAACGAAAATAATAA"
+            ],
+            1066944,
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_lib_format_counts.json:md5,0b0e2dc090e5ad88f9a9d6dbe9c3e4a0"
+                ]
+            ],
+            [
+                "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb",
+                "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:08:35.832206"
+    },
+    "homo_sapiens paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "complete_ref_lens.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "ctable.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "ctg_offsets.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "duplicate_clusters.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "info.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "mphf.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "pos.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "pre_indexing.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "rank.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "refAccumLengths.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "ref_indexing.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "reflengths.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "refseq.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "seq.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "versionInfo.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_meta_info.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_lib_format_counts.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb",
+                    "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd"
+                ],
+                "index": [
+                    [
+                        "complete_ref_lens.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "ctable.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "ctg_offsets.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "duplicate_clusters.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "info.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "mphf.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "pos.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "pre_indexing.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "rank.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "refAccumLengths.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "ref_indexing.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "reflengths.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "refseq.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "seq.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "versionInfo.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json_info": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_meta_info.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "lib_format_counts": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_lib_format_counts.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb",
+                    "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:08:56.819"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/nextflow.config b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/nextflow.config
new file mode 100644
index 000000000..7fc4d632b
--- /dev/null
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: FQ_SUBSAMPLE {
+        ext.args   = '--record-count 1000000 --seed 1'
+    }
+
+}
diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/main.nf b/subworkflows/nf-core/quantify_pseudo_alignment/main.nf
new file mode 100644
index 000000000..b245b9bad
--- /dev/null
+++ b/subworkflows/nf-core/quantify_pseudo_alignment/main.nf
@@ -0,0 +1,123 @@
+//
+// Pseudoalignment and quantification with Salmon or Kallisto
+//
+
+include { SALMON_QUANT     } from '../../../modules/nf-core/salmon/quant'
+include { KALLISTO_QUANT   } from '../../../modules/nf-core/kallisto/quant'
+include { CUSTOM_TX2GENE   } from '../../../modules/nf-core/custom/tx2gene'
+include { TXIMETA_TXIMPORT } from '../../../modules/nf-core/tximeta/tximport'
+
+include { SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT as SE_GENE               } from '../../../modules/nf-core/summarizedexperiment/summarizedexperiment'
+include { SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT as SE_GENE_LENGTH_SCALED } from '../../../modules/nf-core/summarizedexperiment/summarizedexperiment'
+include { SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT as SE_GENE_SCALED        } from '../../../modules/nf-core/summarizedexperiment/summarizedexperiment'
+include { SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT as SE_TRANSCRIPT         } from '../../../modules/nf-core/summarizedexperiment/summarizedexperiment'
+
+workflow QUANTIFY_PSEUDO_ALIGNMENT {
+    take:
+    samplesheet               // channel: [ val(meta), /path/to/samplsheet ]
+    reads                     // channel: [ val(meta), [ reads ] ]
+    index                     // channel: /path/to//index/
+    transcript_fasta          // channel: /path/to/transcript.fasta
+    gtf                       // channel: /path/to/genome.gtf
+    gtf_id_attribute          //     val: GTF gene ID attribute
+    gtf_extra_attribute       //     val: GTF alternative gene attribute (e.g. gene_name)
+    pseudo_aligner            //     val: kallisto or salmon
+    alignment_mode            //    bool: Run Salmon in alignment mode
+    lib_type                  //     val: String to override Salmon library type
+    kallisto_quant_fraglen    //     val: Estimated fragment length required by Kallisto in single-end mode
+    kallisto_quant_fraglen_sd //     val: Estimated standard error for fragment length required by Kallisto in single-end mode
+
+    main:
+    ch_versions = Channel.empty()
+
+    //
+    // Quantify and merge counts across samples
+    //
+    // NOTE: MultiQC needs Salmon outputs, but Kallisto logs
+    if (pseudo_aligner == 'salmon') {
+        SALMON_QUANT (
+            reads,
+            index,
+            gtf,
+            transcript_fasta,
+            alignment_mode,
+            lib_type
+        )
+        ch_pseudo_results = SALMON_QUANT.out.results
+        ch_pseudo_multiqc = ch_pseudo_results
+        ch_versions = ch_versions.mix(SALMON_QUANT.out.versions.first())
+    } else {
+        KALLISTO_QUANT (
+            reads,
+            index,
+            gtf,
+            [],
+            kallisto_quant_fraglen,
+            kallisto_quant_fraglen_sd
+        )
+        ch_pseudo_results = KALLISTO_QUANT.out.results
+        ch_pseudo_multiqc = KALLISTO_QUANT.out.log
+        ch_versions = ch_versions.mix(KALLISTO_QUANT.out.versions.first())
+    }
+
+    CUSTOM_TX2GENE (
+        gtf.map { [ [:], it ] },
+        ch_pseudo_results.collect{ it[1] }.map { [ [:], it ] },
+        pseudo_aligner,
+        gtf_id_attribute,
+        gtf_extra_attribute
+    )
+    ch_versions = ch_versions.mix(CUSTOM_TX2GENE.out.versions)
+
+    TXIMETA_TXIMPORT (
+        ch_pseudo_results.collect{ it[1] }.map { [ ['id': 'all_samples'], it ] },
+        CUSTOM_TX2GENE.out.tx2gene,
+        pseudo_aligner
+    )
+    ch_versions = ch_versions.mix(TXIMETA_TXIMPORT.out.versions)
+
+    SE_GENE (
+        TXIMETA_TXIMPORT.out.counts_gene.concat(TXIMETA_TXIMPORT.out.tpm_gene).groupTuple(),
+        CUSTOM_TX2GENE.out.tx2gene,
+        samplesheet
+    )
+    ch_versions = ch_versions.mix(SE_GENE.out.versions)
+
+    SE_GENE_LENGTH_SCALED (
+        TXIMETA_TXIMPORT.out.counts_gene_length_scaled.concat(TXIMETA_TXIMPORT.out.tpm_gene).groupTuple(),
+        CUSTOM_TX2GENE.out.tx2gene,
+        samplesheet
+    )
+
+    SE_GENE_SCALED (
+        TXIMETA_TXIMPORT.out.counts_gene_scaled.concat(TXIMETA_TXIMPORT.out.tpm_gene).groupTuple(),
+        CUSTOM_TX2GENE.out.tx2gene,
+        samplesheet
+    )
+
+    SE_TRANSCRIPT (
+        TXIMETA_TXIMPORT.out.counts_transcript.concat(TXIMETA_TXIMPORT.out.tpm_transcript).groupTuple(),
+        CUSTOM_TX2GENE.out.tx2gene,
+        samplesheet
+    )
+
+    emit:
+    results                       = ch_pseudo_results                              // channel: [ val(meta), results_dir ]
+    multiqc                       = ch_pseudo_multiqc                              // channel: [ val(meta), files_for_multiqc ]
+
+    tpm_gene                      = TXIMETA_TXIMPORT.out.tpm_gene                  //    path: *gene_tpm.tsv
+    counts_gene                   = TXIMETA_TXIMPORT.out.counts_gene               //    path: *gene_counts.tsv
+    lengths_gene                  = TXIMETA_TXIMPORT.out.lengths_gene              //    path: *gene_lengths.tsv
+    counts_gene_length_scaled     = TXIMETA_TXIMPORT.out.counts_gene_length_scaled //    path: *gene_counts_length_scaled.tsv
+    counts_gene_scaled            = TXIMETA_TXIMPORT.out.counts_gene_scaled        //    path: *gene_counts_scaled.tsv
+    tpm_transcript                = TXIMETA_TXIMPORT.out.tpm_transcript            //    path: *gene_tpm.tsv
+    counts_transcript             = TXIMETA_TXIMPORT.out.counts_transcript         //    path: *transcript_counts.tsv
+    lengths_transcript            = TXIMETA_TXIMPORT.out.lengths_transcript        //    path: *transcript_lengths.tsv
+
+    merged_gene_rds               = SE_GENE.out.rds                                //    path: *.rds
+    merged_gene_rds_length_scaled = SE_GENE_LENGTH_SCALED.out.rds                  //    path: *.rds
+    merged_gene_rds_scaled        = SE_GENE_SCALED.out.rds                         //    path: *.rds
+    merged_transcript_rds         = SE_TRANSCRIPT.out.rds                          //    path: *.rds
+
+    versions                      = ch_versions                                    // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/meta.yml b/subworkflows/nf-core/quantify_pseudo_alignment/meta.yml
new file mode 100644
index 000000000..419bd3cc3
--- /dev/null
+++ b/subworkflows/nf-core/quantify_pseudo_alignment/meta.yml
@@ -0,0 +1,174 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "quantify_pseudo_alignment"
+description: Perform quantification with Salmon or Kallisto to produce count tables and SummarizedExperiment objects
+keywords:
+  - rnaseq
+  - quantification
+  - kallisto
+  - salmon
+components:
+  - custom/tx2gene
+  - kallisto/quant
+  - salmon/quant
+  - summarizedexperiment/summarizedexperiment
+  - tximeta/tximport
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing study-level sample sheet information. e.g. [
+          id:'SRP1234' ].
+  - samplesheet:
+      type: file
+      description: |
+        Sample sheet, to be baked into the `colData` of summarizedexperiment
+        objects.
+      pattern: "*.{csv,tsv}"
+  - reads:
+      type: file
+      description: |
+        Channel with input FastQ files of size 1 and 2 for single-end and
+        paired-end data, respectively. OR a transcriptome-level BAM file if
+        running Salmon in alignment mode.
+  - index:
+      type: path
+      description: |
+        Path to Salmon or Kallisto index in the tool-appropriate form.
+  - gtf:
+      type: file
+      description: |
+        Channel with features in GTF format. Passed to pseudoaligners and used
+        to generate transcript/ gene mappings.
+  - gtf_id_attribute:
+      type: string
+      description: |
+        Attribute in GTF file corresponding to the gene identifier.
+  - gtf_extra_attribute:
+      type: string
+      description: GTF alternative gene attribute (e.g. gene_name)
+  - pseudo_aligner:
+      type: string
+      description: Pseudoaligner, `kallisto` or `salmon`.
+  - alignment_mode:
+      type: boolean
+      description: |
+        If running Salmon, run in alignment mode (`true` or `false`).
+  - lib_type:
+      type: string
+      description: String to override Salmon library type.
+  - kallisto_quant_fraglen:
+      type: integer
+      description: |
+        Estimated fragment length. Required if running Kallisto with
+        single-ended reads.
+  - kallisto_quant_fraglen_sd:
+      type: integer
+      description: |
+        Estimated standard error for fragment length required by Kallisto in
+        single-end mode.
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing study-level sample sheet information. e.g. [
+          id:'SRP1234' ].
+  - results:
+      type: file
+      description: |
+        Channel containing sample-wise results directories from the
+        pseudoaligner.
+  - multiqc:
+      type: file
+      description: |
+        Channel containing those pseudoaligner outputs readable by MultiQC for
+        passing to workflow-level reporting.
+  - tpm_gene:
+      type: file
+      description: |
+        Gene-level matrix of abundance values in TPM.
+      pattern: "*.gene_tpm.tsv"
+  - counts_gene:
+      type: file
+      description: |
+        Gene-level matrix of unadjusted estimated counts from tximport
+        (`countsFromAbundance = 'no'`).
+      pattern: "*.gene_counts.tsv"
+  - lengths_gene:
+      type: file
+      description: |
+        Gene-level matrix of length values for modelling in downstream
+        analysis.
+      pattern: "gene_lengths.tsv"
+  - counts_gene_length_scaled:
+      type: file
+      description: |
+        Gene-level matrix of estimated counts, generated from abundance (TPM)
+        values by scaling to library size, additionally scaled using the
+        average transcript length, averaged over samples and to library size,
+        using tximport `countsFromAbundance = 'lengthScaledTPM'`.
+      pattern: "*.gene_counts_length_scaled.tsv"
+  - counts_gene_scaled:
+      type: file
+      description: |
+        Gene-level matrix of estimated counts, generated from abundance (TPM)
+        values by scaling to library size with tximport `countsFromAbundance =
+        'scaledTPM'`.
+      pattern: "*.gene_counts_length_scaled.tsv"
+  - tpm_transcript:
+      type: file
+      description: |
+        Transcript-level matrix of abundance values in TPM.
+      pattern: "*.transcript_tpm.tsv"
+  - counts_transcript:
+      type: file
+      description: |
+        Transcript-level matrix of unadjusted estimated counts from tximport
+        (`countsFromAbundance = 'no'`).
+      pattern: "*.transcript_counts.tsv"
+  - lengths_transcript:
+      type: file
+      description: |
+        Transcript-level matrix of length values for modelling in downstream
+        analysis.
+      pattern: "transcript_lengths.tsv"
+  - merged_gene_rds:
+      type: file
+      description: |
+        Serialised SummarizedExperiment object containing gene level TPM
+        abundance values and counts generated from tximport with
+        `countsFromAbundance = 'no'`.
+      pattern: "*.rds"
+  - merged_gene_rds_length_scaled:
+      type: file
+      description: |
+        Serialised SummarizedExperiment object containing gene level TPM
+        abundance values and counts generated from tximport with
+        `countsFromAbundance='lengthScaledTPM'`.
+      pattern: "*.rds"
+  - merged_gene_rds_scaled:
+      type: file
+      description: |
+        Serialised SummarizedExperiment object containing gene level TPM
+        abundance values and counts generated from tximport with
+        `countsFromAbundance='scaledTPM'`.
+      pattern: "*.rds"
+  - merged_transcript_rds:
+      type: file
+      description: |
+        Serialised SummarizedExperiment object containing transcript level TPM
+        abundance values and counts generated from tximport with
+        `countsFromAbundance = 'no'`.
+      pattern: "*.rds"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@pinin4fjords"
+  - "@adamrtalbot"
+maintainers:
+  - "@pinin4fjords"
+  - "@adamrtalbot"
diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/nextflow.config b/subworkflows/nf-core/quantify_pseudo_alignment/nextflow.config
new file mode 100644
index 000000000..adf881967
--- /dev/null
+++ b/subworkflows/nf-core/quantify_pseudo_alignment/nextflow.config
@@ -0,0 +1,67 @@
+if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
+    process {
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT' {
+            ext.args   = { params.extra_salmon_quant_args ?: '' }
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') || filename.endsWith('_format_counts.json') ? null : filename }
+            ]
+        }
+    }
+}
+
+if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') {
+    process {
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:KALLISTO_QUANT' {
+            ext.args = params.extra_kallisto_quant_args ?: ''
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.run_info.json') || filename.endsWith('.log') ? null : filename }
+            ]
+        }
+    }
+}
+
+if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
+    process {
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE' {
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT' {
+            ext.prefix = { "${quant_type}.merged" }
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*' {
+            ext.args = '--assay_names counts,abundance'
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.log') ? null : filename }
+            ]
+        }
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts" }
+        }
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_scaled" }
+        }
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_length_scaled" }
+        }
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.transcript_counts" }
+        }
+    }
+}
diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test
new file mode 100644
index 000000000..d0a59629e
--- /dev/null
+++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test
@@ -0,0 +1,242 @@
+nextflow_workflow {
+
+    name "Test Workflow QUANTIFY_PSEUDO_ALIGNMENT"
+    script "../main.nf"
+    workflow "QUANTIFY_PSEUDO_ALIGNMENT"
+
+    test("salmon") {
+
+        setup {
+            run("SALMON_INDEX") {
+                script "../../../../modules/nf-core/salmon/index/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0]  = [
+                    [ id: 'samplesheet' ],
+                    file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/csv/samplesheet_micro.csv', checkIfExists: true)
+                ]
+                input[1]  = [
+                    [ id: 'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[2]  = SALMON_INDEX.out.index
+                input[3]  = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true))
+                input[4]  = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.gtf", checkIfExists: true))
+                input[5]  = 'gene_id'
+                input[6]  = 'gene_name'
+                input[7]  = 'salmon'
+                input[8]  = false
+                input[9]  = 'A'
+                input[10] = null
+                input[11] = null
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                        file(workflow.out.merged_gene_rds[0][1]).name,
+                        file(workflow.out.merged_gene_rds_length_scaled[0][1]).name,
+                        file(workflow.out.merged_gene_rds_scaled[0][1]).name,
+                        file(workflow.out.merged_transcript_rds[0][1]).name,
+                        workflow.out.counts_gene,
+                        workflow.out.counts_gene_length_scaled,
+                        workflow.out.lengths_gene,
+                        workflow.out.lengths_transcript,
+                        workflow.out.merged_counts_transcript,
+                        workflow.out.merged_tpm_transcript,
+                        workflow.out.tpm_gene,
+                        workflow.out.tpm_transcript,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("kallisto") {
+
+        setup {
+            run("KALLISTO_INDEX") {
+                script "../../../../modules/nf-core/kallisto/index/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'transcriptome' ], // meta map
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0]  = [
+                    [ id: 'samplesheet' ],
+                    file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/csv/samplesheet_micro.csv', checkIfExists: true)
+                ]
+                input[1]  = [
+                    [ id: 'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[2]  = KALLISTO_INDEX.out.index
+                input[3]  = Channel.of(file(params.modules_testdata_base_path +  "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true))
+                input[4]  = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.gtf", checkIfExists: true))
+                input[5]  = 'gene_id'
+                input[6]  = 'gene_name'
+                input[7]  = 'kallisto'
+                input[8]  = null
+                input[9]  = null
+                input[10] = []
+                input[11] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                        file(workflow.out.merged_gene_rds[0][1]).name,
+                        file(workflow.out.merged_gene_rds_length_scaled[0][1]).name,
+                        file(workflow.out.merged_gene_rds_scaled[0][1]).name,
+                        file(workflow.out.merged_transcript_rds[0][1]).name,
+                        workflow.out.counts_gene,
+                        workflow.out.counts_gene_length_scaled,
+                        workflow.out.lengths_gene,
+                        workflow.out.lengths_transcript,
+                        workflow.out.tpm_gene,
+                        workflow.out.tpm_transcript,
+                        workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("salmon - stub") {
+
+        options "-stub"
+
+        setup {
+            run("SALMON_INDEX") {
+                script "../../../../modules/nf-core/salmon/index/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)])
+                    input[1] = Channel.of([file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0]  = [
+                    [ id: 'samplesheet' ],
+                    file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/csv/samplesheet_micro.csv', checkIfExists: true)
+                ]
+                input[1]  = [
+                    [ id: 'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[2]  = SALMON_INDEX.out.index
+                input[3]  = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true))
+                input[4]  = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.gtf", checkIfExists: true))
+                input[5]  = 'gene_id'
+                input[6]  = 'gene_name'
+                input[7]  = 'salmon'
+                input[8]  = false
+                input[9]  = 'A'
+                input[10] = null
+                input[11] = null
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+
+    test("kallisto - stub") {
+
+        options "-stub"
+
+        setup {
+            run("KALLISTO_INDEX") {
+                script "../../../../modules/nf-core/kallisto/index/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'transcriptome' ], // meta map
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0]  = [
+                    [ id: 'samplesheet' ],
+                    file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/csv/samplesheet_micro.csv', checkIfExists: true)
+                ]
+                input[1]  = [
+                    [ id: 'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[2]  = KALLISTO_INDEX.out.index
+                input[3]  = Channel.of(file(params.modules_testdata_base_path +  "genomics/homo_sapiens/genome/transcriptome.fasta", checkIfExists: true))
+                input[4]  = Channel.of(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.gtf", checkIfExists: true))
+                input[5]  = 'gene_id'
+                input[6]  = 'gene_name'
+                input[7]  = 'kallisto'
+                input[8]  = null
+                input[9]  = null
+                input[10] = []
+                input[11] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap
new file mode 100644
index 000000000..4db35cced
--- /dev/null
+++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap
@@ -0,0 +1,644 @@
+{
+    "kallisto": {
+        "content": [
+            "all_samples.SummarizedExperiment.rds",
+            "all_samples.SummarizedExperiment.rds",
+            "all_samples.SummarizedExperiment.rds",
+            "all_samples.SummarizedExperiment.rds",
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.gene_counts.tsv:md5,4ba44e5ebc9ed0ca2ca008d10a1dddc3"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.gene_counts_length_scaled.tsv:md5,078746568e3fd0c995559352b661b2d9"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.gene_lengths.tsv:md5,b031192af7a8f64dcc887978a69fdbb7"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.transcript_lengths.tsv:md5,131952a97905469ab012f0f46e52405c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.gene_tpm.tsv:md5,23fa0c64cfbd198806b53897de791b8b"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.transcript_tpm.tsv:md5,de458e1c2a579e53bd7671c5176f5d0c"
+                ]
+            ],
+            [
+                "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96",
+                "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566",
+                "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed",
+                "versions.yml:md5,ea39658f8685118d81d42acd451e66ea"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:36:19.861809"
+    },
+    "salmon - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "13": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "14": [
+                    "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87",
+                    "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a",
+                    "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566",
+                    "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_gene": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_gene_length_scaled": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_gene_scaled": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_transcript": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "lengths_gene": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "lengths_transcript": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_gene_rds": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_gene_rds_length_scaled": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_gene_rds_scaled": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_transcript_rds": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "tpm_gene": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tpm_transcript": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87",
+                    "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a",
+                    "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566",
+                    "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:36:55.281379"
+    },
+    "kallisto - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "13": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "14": [
+                    "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a",
+                    "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566",
+                    "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed",
+                    "versions.yml:md5,ea39658f8685118d81d42acd451e66ea"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_gene": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_gene_length_scaled": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_gene_scaled": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_transcript": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "lengths_gene": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "lengths_transcript": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_gene_rds": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_gene_rds_length_scaled": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_gene_rds_scaled": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_transcript_rds": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.SummarizedExperiment.rds:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "tpm_gene": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tpm_transcript": [
+                    [
+                        {
+                            "id": "all_samples"
+                        },
+                        "all_samples.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a",
+                    "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566",
+                    "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed",
+                    "versions.yml:md5,ea39658f8685118d81d42acd451e66ea"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:37:29.239014"
+    },
+    "salmon": {
+        "content": [
+            "all_samples.SummarizedExperiment.rds",
+            "all_samples.SummarizedExperiment.rds",
+            "all_samples.SummarizedExperiment.rds",
+            "all_samples.SummarizedExperiment.rds",
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.gene_counts.tsv:md5,865a4706b8bf47f476d8298fdd344902"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.gene_counts_length_scaled.tsv:md5,46194b28815747fe3c3d5a619fa994a7"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.gene_lengths.tsv:md5,158e17a7bda7827b3d528f379e81d2bd"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.transcript_lengths.tsv:md5,f39a15fea56a5a8e5776dcdda0c8f102"
+                ]
+            ],
+            null,
+            null,
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.gene_tpm.tsv:md5,9711ed8364c3a1ea4fc87bd5e0780835"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "all_samples"
+                    },
+                    "all_samples.transcript_tpm.tsv:md5,e0c16bf083ebb88bcfaf27cfba12d3e9"
+                ]
+            ],
+            [
+                "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87",
+                "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96",
+                "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566",
+                "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-03T15:35:48.954002"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
new file mode 100644
index 000000000..28e32b200
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -0,0 +1,124 @@
+//
+// Subworkflow with functionality that may be useful for any Nextflow pipeline
+//
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NEXTFLOW_PIPELINE {
+
+    take:
+    print_version        // boolean: print version
+    dump_parameters      // boolean: dump parameters
+    outdir               //    path: base directory used to publish pipeline results
+    check_conda_channels // boolean: check conda channels
+
+    main:
+
+    //
+    // Print workflow version and exit on --version
+    //
+    if (print_version) {
+        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        System.exit(0)
+    }
+
+    //
+    // Dump pipeline parameters to a JSON file
+    //
+    if (dump_parameters && outdir) {
+        dumpParametersToJSON(outdir)
+    }
+
+    //
+    // When running with Conda, warn if channels have not been set-up appropriately
+    //
+    if (check_conda_channels) {
+        checkCondaChannels()
+    }
+
+    emit:
+    dummy_emit = true
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+// Generate version string
+//
+def getWorkflowVersion() {
+    def version_string = "" as String
+    if (workflow.manifest.version) {
+        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+        version_string += "${prefix_v}${workflow.manifest.version}"
+    }
+
+    if (workflow.commitId) {
+        def git_shortsha = workflow.commitId.substring(0, 7)
+        version_string += "-g${git_shortsha}"
+    }
+
+    return version_string
+}
+
+//
+// Dump pipeline parameters to a JSON file
+//
+def dumpParametersToJSON(outdir) {
+    def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+    def filename   = "params_${timestamp}.json"
+    def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
+    def jsonStr    = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
+
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    temp_pf.delete()
+}
+
+//
+// When running with -profile conda, warn if channels have not been set-up appropriately
+//
+def checkCondaChannels() {
+    def parser = new org.yaml.snakeyaml.Yaml()
+    def channels = []
+    try {
+        def config = parser.load("conda config --show channels".execute().text)
+        channels = config.channels
+    } catch(NullPointerException | IOException e) {
+        log.warn "Could not verify conda channel configuration."
+        return
+    }
+
+    // Check that all channels are present
+    // This channel list is ordered by required channel priority.
+    def required_channels_in_order = ['conda-forge', 'bioconda']
+    def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
+
+    // Check that they are in the right order
+    def channel_priority_violation = false
+
+    required_channels_in_order.eachWithIndex { channel, index ->
+        if (index < required_channels_in_order.size() - 1) {
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+        }
+    }
+
+    if (channels_missing | channel_priority_violation) {
+        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            "  There is a problem with your Conda configuration!\n\n" +
+            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
+            "  Please refer to https://bioconda.github.io/\n" +
+            "  The observed channel order is \n" +
+            "  ${channels}\n" +
+            "  but the following channel order is required:\n" +
+            "  ${required_channels_in_order}\n" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+    }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
new file mode 100644
index 000000000..e5c3a0a82
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
@@ -0,0 +1,38 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NEXTFLOW_PIPELINE"
+description: Subworkflow with functionality that may be useful for any Nextflow pipeline
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - version
+components: []
+input:
+  - print_version:
+      type: boolean
+      description: |
+        Print the version of the pipeline and exit
+  - dump_parameters:
+      type: boolean
+      description: |
+        Dump the parameters of the pipeline to a JSON file
+  - output_directory:
+      type: directory
+      description: Path to output dir to write JSON file to.
+      pattern: "results/"
+  - check_conda_channel:
+      type: boolean
+      description: |
+        Check if the conda channel priority is correct.
+output:
+  - dummy_emit:
+      type: boolean
+      description: |
+        Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@adamrtalbot"
+  - "@drpatelh"
+maintainers:
+  - "@adamrtalbot"
+  - "@drpatelh"
+  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
new file mode 100644
index 000000000..742d4a00a
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
@@ -0,0 +1,51 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
+    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
+
+    test("Test Function getWorkflowVersion") {
+
+        function "getWorkflowVersion"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function dumpParametersToJSON") {
+
+        function "dumpParametersToJSON"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                input[0] = "$outputDir"
+                """.stripIndent()
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success }
+            )
+        }
+    }
+
+    test("Test Function checkCondaChannels") {
+
+        function "checkCondaChannels"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
new file mode 100644
index 000000000..e3f0baf47
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,20 @@
+{
+    "Test Function getWorkflowVersion": {
+        "content": [
+            "v9.9.9"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:05.308243"
+    },
+    "Test Function checkCondaChannels": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:12.425833"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
new file mode 100644
index 000000000..13782037c
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,108 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NEXTFLOW_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
+    workflow "UTILS_NEXTFLOW_PIPELINE"
+
+    test("Should run no inputs") {
+
+        when {
+            workflow {
+                """
+                print_version        = false
+                dump_parameters      = false
+                outdir               = null
+                check_conda_channels = false
+
+                input[0] = print_version
+                input[1] = dump_parameters
+                input[2] = outdir
+                input[3] = check_conda_channels
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should print version") {
+
+        when {
+            workflow {
+                """
+                print_version        = true
+                dump_parameters      = false
+                outdir               = null
+                check_conda_channels = false
+
+                input[0] = print_version
+                input[1] = dump_parameters
+                input[2] = outdir
+                input[3] = check_conda_channels
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
+            )
+        }
+    }
+
+    test("Should dump params") {
+
+        when {
+            workflow {
+                """
+                print_version        = false
+                dump_parameters      = true
+                outdir               = 'results'
+                check_conda_channels = false
+
+                input[0] = false
+                input[1] = true
+                input[2] = outdir
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should not create params JSON if no output directory") {
+
+        when {
+            workflow {
+                """
+                print_version        = false
+                dump_parameters      = true
+                outdir               = null
+                check_conda_channels = false
+
+                input[0] = false
+                input[1] = true
+                input[2] = outdir
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
new file mode 100644
index 000000000..a09572e5b
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+    name            = 'nextflow_workflow'
+    author          = """nf-core"""
+    homePage        = 'https://127.0.0.1'
+    description     = """Dummy pipeline"""
+    nextflowVersion = '!>=23.04.0'
+    version         = '9.9.9'
+    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
new file mode 100644
index 000000000..cbd8495bb
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -0,0 +1,445 @@
+//
+// Subworkflow with utility functions specific to the nf-core pipeline template
+//
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFCORE_PIPELINE {
+
+    take:
+    nextflow_cli_args
+
+    main:
+    valid_config = checkConfigProvided()
+    checkProfileProvided(nextflow_cli_args)
+
+    emit:
+    valid_config
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+//  Warn if a -profile or Nextflow config has not been provided to run the pipeline
+//
+def checkConfigProvided() {
+    def valid_config = true as Boolean
+    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
+            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+            "Please refer to the quick start section and usage docs for the pipeline.\n "
+        valid_config = false
+    }
+    return valid_config
+}
+
+//
+// Exit pipeline if --profile contains spaces
+//
+def checkProfileProvided(nextflow_cli_args) {
+    if (workflow.profile.endsWith(',')) {
+        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
+            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+    }
+    if (nextflow_cli_args[0]) {
+        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
+            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+    }
+}
+
+//
+// Citation string for pipeline
+//
+def workflowCitation() {
+    def temp_doi_ref = ""
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    }
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+        "* The pipeline\n" +
+        temp_doi_ref + "\n" +
+        "* The nf-core framework\n" +
+        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+        "* Software dependencies\n" +
+        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+}
+
+//
+// Generate workflow version string
+//
+def getWorkflowVersion() {
+    def version_string = "" as String
+    if (workflow.manifest.version) {
+        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+        version_string += "${prefix_v}${workflow.manifest.version}"
+    }
+
+    if (workflow.commitId) {
+        def git_shortsha = workflow.commitId.substring(0, 7)
+        version_string += "-g${git_shortsha}"
+    }
+
+    return version_string
+}
+
+//
+// Get software versions for pipeline
+//
+def processVersionsFromYAML(yaml_file) {
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    return yaml.dumpAsMap(versions).trim()
+}
+
+//
+// Get workflow version for pipeline
+//
+def workflowVersionToYAML() {
+    return """
+    Workflow:
+        $workflow.manifest.name: ${getWorkflowVersion()}
+        Nextflow: $workflow.nextflow.version
+    """.stripIndent().trim()
+}
+
+//
+// Get channel of software versions used in pipeline in YAML format
+//
+def softwareVersionsToYAML(ch_versions) {
+    return ch_versions
+                .unique()
+                .map { version -> processVersionsFromYAML(version) }
+                .unique()
+                .mix(Channel.of(workflowVersionToYAML()))
+}
+
+//
+// Get workflow summary for MultiQC
+//
+def paramsSummaryMultiqc(summary_params) {
+    def summary_section = ''
+    summary_params.keySet().each { group ->
+        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
+        if (group_params) {
+            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
+            summary_section += "    <dl class=\"dl-horizontal\">\n"
+            group_params.keySet().sort().each { param ->
+                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+            }
+            summary_section += "    </dl>\n"
+        }
+    }
+
+    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
+    yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text        += "plot_type: 'html'\n"
+    yaml_file_text        += "data: |\n"
+    yaml_file_text        += "${summary_section}"
+
+    return yaml_file_text
+}
+
+//
+// nf-core logo
+//
+def nfCoreLogo(monochrome_logs=true) {
+    def colors = logColours(monochrome_logs) as Map
+    String.format(
+        """\n
+        ${dashedLine(monochrome_logs)}
+                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                ${colors.green}`._,._,\'${colors.reset}
+        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
+        ${dashedLine(monochrome_logs)}
+        """.stripIndent()
+    )
+}
+
+//
+// Return dashed line
+//
+def dashedLine(monochrome_logs=true) {
+    def colors = logColours(monochrome_logs) as Map
+    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+}
+
+//
+// ANSII colours used for terminal logging
+//
+def logColours(monochrome_logs=true) {
+    def colorcodes = [:] as Map
+
+    // Reset / Meta
+    colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
+    colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
+    colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
+    colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+    colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
+    colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
+    colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
+
+    // Regular Colors
+    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+
+    // Bold
+    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+
+    // Underline
+    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+
+    // High Intensity
+    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+
+    // Bold High Intensity
+    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+
+    return colorcodes
+}
+
+//
+// Attach the multiqc report to email
+//
+def attachMultiqcReport(multiqc_report) {
+    def mqc_report = null
+    try {
+        if (workflow.success) {
+            mqc_report = multiqc_report.getVal()
+            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+                if (mqc_report.size() > 1) {
+                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                }
+                mqc_report = mqc_report[0]
+            }
+        }
+    } catch (all) {
+        if (multiqc_report) {
+            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+        }
+    }
+    return mqc_report
+}
+
+//
+// Construct and send completion email
+//
+def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
+
+    // Set up the e-mail variables
+    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    if (!workflow.success) {
+        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+    }
+
+    def summary = [:]
+    summary_params.keySet().sort().each { group ->
+        summary << summary_params[group]
+    }
+
+    def misc_fields = [:]
+    misc_fields['Date Started']              = workflow.start
+    misc_fields['Date Completed']            = workflow.complete
+    misc_fields['Pipeline script file path'] = workflow.scriptFile
+    misc_fields['Pipeline script hash ID']   = workflow.scriptId
+    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
+    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    misc_fields['Nextflow Version']           = workflow.nextflow.version
+    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+    def email_fields = [:]
+    email_fields['version']      = getWorkflowVersion()
+    email_fields['runName']      = workflow.runName
+    email_fields['success']      = workflow.success
+    email_fields['dateComplete'] = workflow.complete
+    email_fields['duration']     = workflow.duration
+    email_fields['exitStatus']   = workflow.exitStatus
+    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    email_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    email_fields['commandLine']  = workflow.commandLine
+    email_fields['projectDir']   = workflow.projectDir
+    email_fields['summary']      = summary << misc_fields
+
+    // On success try attach the multiqc report
+    def mqc_report = attachMultiqcReport(multiqc_report)
+
+    // Check if we are only sending emails on failure
+    def email_address = email
+    if (!email && email_on_fail && !workflow.success) {
+        email_address = email_on_fail
+    }
+
+    // Render the TXT template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    def tf           = new File("${workflow.projectDir}/assets/email_template.txt")
+    def txt_template = engine.createTemplate(tf).make(email_fields)
+    def email_txt    = txt_template.toString()
+
+    // Render the HTML template
+    def hf            = new File("${workflow.projectDir}/assets/email_template.html")
+    def html_template = engine.createTemplate(hf).make(email_fields)
+    def email_html    = html_template.toString()
+
+    // Render the sendmail template
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
+    def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+    def sendmail_html          = sendmail_template.toString()
+
+    // Send the HTML e-mail
+    def colors = logColours(monochrome_logs) as Map
+    if (email_address) {
+        try {
+            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
+            // Try to send HTML e-mail using sendmail
+            def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+            sendmail_tf.withWriter { w -> w << sendmail_html }
+            [ 'sendmail', '-t' ].execute() << sendmail_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+        } catch (all) {
+            // Catch failures and try with plaintext
+            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            mail_cmd.execute() << email_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+        }
+    }
+
+    // Write summary e-mail HTML to a file
+    def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
+    output_hf.withWriter { w -> w << email_html }
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    output_hf.delete()
+
+    // Write summary e-mail TXT to a file
+    def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
+    output_tf.withWriter { w -> w << email_txt }
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    output_tf.delete()
+}
+
+//
+// Print pipeline summary on completion
+//
+def completionSummary(monochrome_logs=true) {
+    def colors = logColours(monochrome_logs) as Map
+    if (workflow.success) {
+        if (workflow.stats.ignoredCount == 0) {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
+        } else {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+        }
+    } else {
+        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+    }
+}
+
+//
+// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
+//
+def imNotification(summary_params, hook_url) {
+    def summary = [:]
+    summary_params.keySet().sort().each { group ->
+        summary << summary_params[group]
+    }
+
+    def misc_fields = [:]
+    misc_fields['start']                                = workflow.start
+    misc_fields['complete']                             = workflow.complete
+    misc_fields['scriptfile']                           = workflow.scriptFile
+    misc_fields['scriptid']                             = workflow.scriptId
+    if (workflow.repository) misc_fields['repository']  = workflow.repository
+    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
+    if (workflow.revision)   misc_fields['revision']    = workflow.revision
+    misc_fields['nxf_version']                          = workflow.nextflow.version
+    misc_fields['nxf_build']                            = workflow.nextflow.build
+    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+
+    def msg_fields = [:]
+    msg_fields['version']      = getWorkflowVersion()
+    msg_fields['runName']      = workflow.runName
+    msg_fields['success']      = workflow.success
+    msg_fields['dateComplete'] = workflow.complete
+    msg_fields['duration']     = workflow.duration
+    msg_fields['exitStatus']   = workflow.exitStatus
+    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
+    msg_fields['projectDir']   = workflow.projectDir
+    msg_fields['summary']      = summary << misc_fields
+
+    // Render the JSON template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    // Different JSON depending on the service provider
+    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
+    def json_template = engine.createTemplate(hf).make(msg_fields)
+    def json_message  = json_template.toString()
+
+    // POST
+    def post = new URL(hook_url).openConnection();
+    post.setRequestMethod("POST")
+    post.setDoOutput(true)
+    post.setRequestProperty("Content-Type", "application/json")
+    post.getOutputStream().write(json_message.getBytes("UTF-8"));
+    def postRC = post.getResponseCode();
+    if (! postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText());
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
new file mode 100644
index 000000000..d08d24342
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
@@ -0,0 +1,24 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFCORE_PIPELINE"
+description: Subworkflow with utility functions specific to the nf-core pipeline template
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - version
+components: []
+input:
+  - nextflow_cli_args:
+      type: list
+      description: |
+        Nextflow CLI positional arguments
+output:
+  - success:
+      type: boolean
+      description: |
+        Dummy output to indicate success
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
+  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
new file mode 100644
index 000000000..3de07f37a
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -0,0 +1,130 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+
+    test("Test Function checkConfigProvided") {
+
+        function "checkConfigProvided"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function checkProfileProvided") {
+
+        function "checkProfileProvided"
+
+        when {
+            function {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function workflowCitation") {
+
+        function "workflowCitation"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function nfCoreLogo") {
+
+        function "nfCoreLogo"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function dashedLine") {
+
+        function "dashedLine"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function without logColours") {
+
+        function "logColours"
+
+        when {
+            function {
+                """
+                input[0] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function with logColours") {
+        function "logColours"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
new file mode 100644
index 000000000..1037232c9
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,166 @@
+{
+    "Test Function checkProfileProvided": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:03.360873"
+    },
+    "Test Function checkConfigProvided": {
+        "content": [
+            true
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:59.729647"
+    },
+    "Test Function nfCoreLogo": {
+        "content": [
+            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:10.562934"
+    },
+    "Test Function workflowCitation": {
+        "content": [
+            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:07.019761"
+    },
+    "Test Function without logColours": {
+        "content": [
+            {
+                "reset": "",
+                "bold": "",
+                "dim": "",
+                "underlined": "",
+                "blink": "",
+                "reverse": "",
+                "hidden": "",
+                "black": "",
+                "red": "",
+                "green": "",
+                "yellow": "",
+                "blue": "",
+                "purple": "",
+                "cyan": "",
+                "white": "",
+                "bblack": "",
+                "bred": "",
+                "bgreen": "",
+                "byellow": "",
+                "bblue": "",
+                "bpurple": "",
+                "bcyan": "",
+                "bwhite": "",
+                "ublack": "",
+                "ured": "",
+                "ugreen": "",
+                "uyellow": "",
+                "ublue": "",
+                "upurple": "",
+                "ucyan": "",
+                "uwhite": "",
+                "iblack": "",
+                "ired": "",
+                "igreen": "",
+                "iyellow": "",
+                "iblue": "",
+                "ipurple": "",
+                "icyan": "",
+                "iwhite": "",
+                "biblack": "",
+                "bired": "",
+                "bigreen": "",
+                "biyellow": "",
+                "biblue": "",
+                "bipurple": "",
+                "bicyan": "",
+                "biwhite": ""
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:17.969323"
+    },
+    "Test Function dashedLine": {
+        "content": [
+            "-\u001b[2m----------------------------------------------------\u001b[0m-"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:14.366181"
+    },
+    "Test Function with logColours": {
+        "content": [
+            {
+                "reset": "\u001b[0m",
+                "bold": "\u001b[1m",
+                "dim": "\u001b[2m",
+                "underlined": "\u001b[4m",
+                "blink": "\u001b[5m",
+                "reverse": "\u001b[7m",
+                "hidden": "\u001b[8m",
+                "black": "\u001b[0;30m",
+                "red": "\u001b[0;31m",
+                "green": "\u001b[0;32m",
+                "yellow": "\u001b[0;33m",
+                "blue": "\u001b[0;34m",
+                "purple": "\u001b[0;35m",
+                "cyan": "\u001b[0;36m",
+                "white": "\u001b[0;37m",
+                "bblack": "\u001b[1;30m",
+                "bred": "\u001b[1;31m",
+                "bgreen": "\u001b[1;32m",
+                "byellow": "\u001b[1;33m",
+                "bblue": "\u001b[1;34m",
+                "bpurple": "\u001b[1;35m",
+                "bcyan": "\u001b[1;36m",
+                "bwhite": "\u001b[1;37m",
+                "ublack": "\u001b[4;30m",
+                "ured": "\u001b[4;31m",
+                "ugreen": "\u001b[4;32m",
+                "uyellow": "\u001b[4;33m",
+                "ublue": "\u001b[4;34m",
+                "upurple": "\u001b[4;35m",
+                "ucyan": "\u001b[4;36m",
+                "uwhite": "\u001b[4;37m",
+                "iblack": "\u001b[0;90m",
+                "ired": "\u001b[0;91m",
+                "igreen": "\u001b[0;92m",
+                "iyellow": "\u001b[0;93m",
+                "iblue": "\u001b[0;94m",
+                "ipurple": "\u001b[0;95m",
+                "icyan": "\u001b[0;96m",
+                "iwhite": "\u001b[0;97m",
+                "biblack": "\u001b[1;90m",
+                "bired": "\u001b[1;91m",
+                "bigreen": "\u001b[1;92m",
+                "biyellow": "\u001b[1;93m",
+                "biblue": "\u001b[1;94m",
+                "bipurple": "\u001b[1;95m",
+                "bicyan": "\u001b[1;96m",
+                "biwhite": "\u001b[1;97m"
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:21.714424"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
new file mode 100644
index 000000000..ff1ae72a9
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,25 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFCORE_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    workflow "UTILS_NFCORE_PIPELINE"
+
+    test("Should run without failures") {
+
+        when {
+            workflow {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
new file mode 100644
index 000000000..859d1030f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
@@ -0,0 +1,19 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "valid_config": [
+                    true
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:25.726491"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
new file mode 100644
index 000000000..d0a926bf6
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+    name            = 'nextflow_workflow'
+    author          = """nf-core"""
+    homePage        = 'https://127.0.0.1'
+    description     = """Dummy pipeline"""
+    nextflowVersion  = '!>=23.04.0'
+    version         = '9.9.9'
+    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
new file mode 100644
index 000000000..2585b65d1
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
@@ -0,0 +1,62 @@
+//
+// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
+//
+
+/*
+========================================================================================
+    IMPORT NF-VALIDATION PLUGIN
+========================================================================================
+*/
+
+include { paramsHelp         } from 'plugin/nf-validation'
+include { paramsSummaryLog   } from 'plugin/nf-validation'
+include { validateParameters } from 'plugin/nf-validation'
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFVALIDATION_PLUGIN {
+
+    take:
+    print_help       // boolean: print help
+    workflow_command //  string: default commmand used to run pipeline
+    pre_help_text    //  string: string to be printed before help text and summary log
+    post_help_text   //  string: string to be printed after help text and summary log
+    validate_params  // boolean: validate parameters
+    schema_filename  //    path: JSON schema file, null to use default value
+
+    main:
+
+    log.debug "Using schema file: ${schema_filename}"
+
+    // Default values for strings
+    pre_help_text    = pre_help_text    ?: ''
+    post_help_text   = post_help_text   ?: ''
+    workflow_command = workflow_command ?: ''
+
+    //
+    // Print help message if needed
+    //
+    if (print_help) {
+        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
+        System.exit(0)
+    }
+
+    //
+    // Print parameter summary to stdout
+    //
+    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
+
+    //
+    // Validate parameters relative to the parameter JSON schema
+    //
+    if (validate_params){
+        validateParameters(parameters_schema: schema_filename)
+    }
+
+    emit:
+    dummy_emit = true
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
new file mode 100644
index 000000000..3d4a6b04f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
@@ -0,0 +1,44 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFVALIDATION_PLUGIN"
+description: Use nf-validation to initiate and validate a pipeline
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - validation
+components: []
+input:
+  - print_help:
+      type: boolean
+      description: |
+        Print help message and exit
+  - workflow_command:
+      type: string
+      description: |
+        The command to run the workflow e.g. "nextflow run main.nf"
+  - pre_help_text:
+      type: string
+      description: |
+        Text to print before the help message
+  - post_help_text:
+      type: string
+      description: |
+        Text to print after the help message
+  - validate_params:
+      type: boolean
+      description: |
+        Validate the parameters and error if invalid.
+  - schema_filename:
+      type: string
+      description: |
+        The filename of the schema to validate against.
+output:
+  - dummy_emit:
+      type: boolean
+      description: |
+        Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
+  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
new file mode 100644
index 000000000..5649654e6
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -0,0 +1,194 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFVALIDATION_PLUGIN"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+
+            workflow {
+                """
+                help             = false
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should run help") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.exitStatus == 0 },
+                { assert workflow.stdout.any { it.contains('Input/output options') } },
+                { assert workflow.stdout.any { it.contains('--outdir') } }
+            )
+        }
+    }
+
+    test("Should run help with command") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = "nextflow run noorg/doesntexist"
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.exitStatus == 0 },
+                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
+                { assert workflow.stdout.any { it.contains('Input/output options') } },
+                { assert workflow.stdout.any { it.contains('--outdir') } }
+            )
+        }
+    }
+
+    test("Should run help with extra text") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = "nextflow run noorg/doesntexist"
+                pre_help_text    = "pre-help-text"
+                post_help_text   = "post-help-text"
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.exitStatus == 0 },
+                { assert workflow.stdout.any { it.contains('pre-help-text') } },
+                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
+                { assert workflow.stdout.any { it.contains('Input/output options') } },
+                { assert workflow.stdout.any { it.contains('--outdir') } },
+                { assert workflow.stdout.any { it.contains('post-help-text') } }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+                outdir          = 1
+            }
+            workflow {
+                """
+                help             = false
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = true
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
new file mode 100644
index 000000000..7626c1c93
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
@@ -0,0 +1,96 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+    "title": ". pipeline parameters",
+    "description": "",
+    "type": "object",
+    "definitions": {
+        "input_output_options": {
+            "title": "Input/output options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Define where the pipeline should find input data and save output data.",
+            "required": ["outdir"],
+            "properties": {
+                "validate_params": {
+                    "type": "boolean",
+                    "description": "Validate parameters?",
+                    "default": true,
+                    "hidden": true
+                },
+                "outdir": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+                    "fa_icon": "fas fa-folder-open"
+                },
+                "test_data_base": {
+                    "type": "string",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules",
+                    "description": "Base for test data directory",
+                    "hidden": true
+                },
+                "test_data": {
+                    "type": "string",
+                    "description": "Fake test data param",
+                    "hidden": true
+                }
+            }
+        },
+        "generic_options": {
+            "title": "Generic options",
+            "type": "object",
+            "fa_icon": "fas fa-file-import",
+            "description": "Less common options for the pipeline, typically set in a config file.",
+            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+            "properties": {
+                "help": {
+                    "type": "boolean",
+                    "description": "Display help text.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
+                "version": {
+                    "type": "boolean",
+                    "description": "Display version and exit.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
+                "logo": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Display nf-core logo in console output.",
+                    "fa_icon": "fas fa-image",
+                    "hidden": true
+                },
+                "singularity_pull_docker_container": {
+                    "type": "boolean",
+                    "description": "Pull Singularity container from Docker?",
+                    "hidden": true
+                },
+                "publish_dir_mode": {
+                    "type": "string",
+                    "default": "copy",
+                    "description": "Method used to save pipeline results to output directory.",
+                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
+                    "fa_icon": "fas fa-copy",
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "hidden": true
+                },
+                "monochrome_logs": {
+                    "type": "boolean",
+                    "description": "Use monochrome_logs",
+                    "hidden": true
+                }
+            }
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/input_output_options"
+        },
+        {
+            "$ref": "#/definitions/generic_options"
+        }
+    ]
+}
diff --git a/tests/default.nf.test b/tests/default.nf.test
new file mode 100644
index 000000000..069bb846f
--- /dev/null
+++ b/tests/default.nf.test
@@ -0,0 +1,961 @@
+nextflow_pipeline {
+
+    name "Test pipeline with default settings"
+    script "../main.nf"
+
+    test("Params: default") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name
+                ).match("fastqc/raw") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name
+                ).match("fastqc/trim") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name
+                ).match("salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.sf").name
+                ).match("salmon_quant") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name
+                ).match("star_salmon/bigwig") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name
+                ).match("star_salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"),
+                    // PDFs are not stable
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name
+                ).match("star_salmon/dupradar") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"),
+                    // These files are unstable
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary").name
+                ).match("star_salmon/featurecounts") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"),
+                    // Logs are not stable
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name
+                ).match("star_salmon/log") },
+                { assert snapshot(
+                    // Metrics are not stable
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name
+                ).match("star_salmon/picard_metrics") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    // HTML reports and these files are not stable
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name
+                ).match("star_salmon/qualimap") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"),
+                    // PDFs, R scripts and all these files are not stable
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name
+                ).match("star_salmon/rseqc") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("star_salmon/salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name
+                ).match("star_salmon/samtools_stats") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name
+                ).match("star_salmon/stringtie") },
+                { assert snapshot(
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name
+                ).match("star_salmon/markdup") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name
+                ).match("star_salmon/salmon_quant") },
+                { assert snapshot(
+                    // These reports are not stable
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match("trimgalore") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    test("Params: default - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    file("${params.outdir}/custom/out/genome_transcriptome.fasta").name,
+                    file("${params.outdir}/custom/out/genome_transcriptome.gtf").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
new file mode 100644
index 000000000..9be7dfb04
--- /dev/null
+++ b/tests/default.nf.test.snap
@@ -0,0 +1,1080 @@
+{
+    "star_salmon/log": {
+        "content": [
+            "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee",
+            "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8",
+            "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
+            "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204",
+            "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23",
+            "RAP1_IAA_30M_REP1.Log.final.out",
+            "RAP1_IAA_30M_REP1.Log.out",
+            "RAP1_IAA_30M_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP1.Log.final.out",
+            "RAP1_UNINDUCED_REP1.Log.out",
+            "RAP1_UNINDUCED_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP2.Log.final.out",
+            "RAP1_UNINDUCED_REP2.Log.out",
+            "RAP1_UNINDUCED_REP2.Log.progress.out",
+            "WT_REP1.Log.final.out",
+            "WT_REP1.Log.out",
+            "WT_REP1.Log.progress.out",
+            "WT_REP2.Log.final.out",
+            "WT_REP2.Log.out",
+            "WT_REP2.Log.progress.out"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T14:57:58.85709"
+    },
+    "star_salmon/salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020",
+            "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5",
+            "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748",
+            "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde",
+            "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae",
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T13:24:55.413942"
+    },
+    "trimgalore": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T13:59:56.824816"
+    },
+    "star_salmon/rseqc": {
+        "content": [
+            "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33",
+            "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,2ca0ce0fd3204bd2cc4812c4655b1f1f",
+            "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40",
+            "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d",
+            "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14",
+            "RAP1_IAA_30M_REP1.bam_stat.txt",
+            "RAP1_UNINDUCED_REP1.bam_stat.txt",
+            "RAP1_UNINDUCED_REP2.bam_stat.txt",
+            "WT_REP1.bam_stat.txt",
+            "WT_REP2.bam_stat.txt",
+            "RAP1_IAA_30M_REP1.inner_distance_plot.pdf",
+            "WT_REP1.inner_distance_plot.pdf",
+            "WT_REP2.inner_distance_plot.pdf",
+            "RAP1_IAA_30M_REP1.inner_distance_plot.r",
+            "WT_REP1.inner_distance_plot.r",
+            "WT_REP2.inner_distance_plot.r",
+            "RAP1_IAA_30M_REP1.inner_distance.txt",
+            "RAP1_IAA_30M_REP1.inner_distance_freq.txt",
+            "RAP1_IAA_30M_REP1.inner_distance_mean.txt",
+            "WT_REP1.inner_distance.txt",
+            "WT_REP1.inner_distance_freq.txt",
+            "WT_REP1.inner_distance_mean.txt",
+            "WT_REP2.inner_distance.txt",
+            "WT_REP2.inner_distance_freq.txt",
+            "WT_REP2.inner_distance_mean.txt",
+            "RAP1_IAA_30M_REP1.junction.Interact.bed",
+            "RAP1_IAA_30M_REP1.junction.bed",
+            "RAP1_UNINDUCED_REP1.junction.Interact.bed",
+            "RAP1_UNINDUCED_REP1.junction.bed",
+            "RAP1_UNINDUCED_REP2.junction.Interact.bed",
+            "RAP1_UNINDUCED_REP2.junction.bed",
+            "WT_REP1.junction.Interact.bed",
+            "WT_REP1.junction.bed",
+            "WT_REP2.junction.Interact.bed",
+            "WT_REP2.junction.bed",
+            "RAP1_IAA_30M_REP1.junction_annotation.log",
+            "RAP1_UNINDUCED_REP1.junction_annotation.log",
+            "RAP1_UNINDUCED_REP2.junction_annotation.log",
+            "WT_REP1.junction_annotation.log",
+            "WT_REP2.junction_annotation.log",
+            "RAP1_IAA_30M_REP1.splice_events.pdf",
+            "RAP1_IAA_30M_REP1.splice_junction.pdf",
+            "RAP1_UNINDUCED_REP1.splice_events.pdf",
+            "RAP1_UNINDUCED_REP1.splice_junction.pdf",
+            "RAP1_UNINDUCED_REP2.splice_events.pdf",
+            "RAP1_UNINDUCED_REP2.splice_junction.pdf",
+            "WT_REP1.splice_events.pdf",
+            "WT_REP1.splice_junction.pdf",
+            "WT_REP2.splice_events.pdf",
+            "WT_REP2.splice_junction.pdf",
+            "RAP1_IAA_30M_REP1.junction_plot.r",
+            "RAP1_UNINDUCED_REP1.junction_plot.r",
+            "RAP1_UNINDUCED_REP2.junction_plot.r",
+            "WT_REP1.junction_plot.r",
+            "WT_REP2.junction_plot.r",
+            "RAP1_IAA_30M_REP1.junction.xls",
+            "RAP1_UNINDUCED_REP1.junction.xls",
+            "RAP1_UNINDUCED_REP2.junction.xls",
+            "WT_REP1.junction.xls",
+            "WT_REP2.junction.xls",
+            "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf",
+            "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf",
+            "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf",
+            "WT_REP1.junctionSaturation_plot.pdf",
+            "WT_REP2.junctionSaturation_plot.pdf",
+            "RAP1_IAA_30M_REP1.junctionSaturation_plot.r",
+            "RAP1_UNINDUCED_REP1.junctionSaturation_plot.r",
+            "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r",
+            "WT_REP1.junctionSaturation_plot.r",
+            "WT_REP2.junctionSaturation_plot.r",
+            "RAP1_IAA_30M_REP1.read_distribution.txt",
+            "RAP1_UNINDUCED_REP1.read_distribution.txt",
+            "RAP1_UNINDUCED_REP2.read_distribution.txt",
+            "WT_REP1.read_distribution.txt",
+            "WT_REP2.read_distribution.txt",
+            "RAP1_IAA_30M_REP1.DupRate_plot.pdf",
+            "RAP1_UNINDUCED_REP1.DupRate_plot.pdf",
+            "RAP1_UNINDUCED_REP2.DupRate_plot.pdf",
+            "WT_REP1.DupRate_plot.pdf",
+            "WT_REP2.DupRate_plot.pdf",
+            "RAP1_IAA_30M_REP1.DupRate_plot.r",
+            "RAP1_UNINDUCED_REP1.DupRate_plot.r",
+            "RAP1_UNINDUCED_REP2.DupRate_plot.r",
+            "WT_REP1.DupRate_plot.r",
+            "WT_REP2.DupRate_plot.r",
+            "RAP1_IAA_30M_REP1.pos.DupRate.xls",
+            "RAP1_IAA_30M_REP1.seq.DupRate.xls",
+            "RAP1_UNINDUCED_REP1.pos.DupRate.xls",
+            "RAP1_UNINDUCED_REP1.seq.DupRate.xls",
+            "RAP1_UNINDUCED_REP2.pos.DupRate.xls",
+            "RAP1_UNINDUCED_REP2.seq.DupRate.xls",
+            "WT_REP1.pos.DupRate.xls",
+            "WT_REP1.seq.DupRate.xls",
+            "WT_REP2.pos.DupRate.xls",
+            "WT_REP2.seq.DupRate.xls"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:44:57.857714"
+    },
+    "references": {
+        "content": [
+            "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
+            "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T13:59:53.18077"
+    },
+    "star_salmon/samtools_stats": {
+        "content": [
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat",
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats",
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats",
+            "RAP1_IAA_30M_REP1.sorted.bam.flagstat",
+            "RAP1_IAA_30M_REP1.sorted.bam.idxstats",
+            "RAP1_IAA_30M_REP1.sorted.bam.stats",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats",
+            "RAP1_UNINDUCED_REP1.sorted.bam.flagstat",
+            "RAP1_UNINDUCED_REP1.sorted.bam.idxstats",
+            "RAP1_UNINDUCED_REP1.sorted.bam.stats",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats",
+            "RAP1_UNINDUCED_REP2.sorted.bam.flagstat",
+            "RAP1_UNINDUCED_REP2.sorted.bam.idxstats",
+            "RAP1_UNINDUCED_REP2.sorted.bam.stats",
+            "WT_REP1.markdup.sorted.bam.flagstat",
+            "WT_REP1.markdup.sorted.bam.idxstats",
+            "WT_REP1.markdup.sorted.bam.stats",
+            "WT_REP1.sorted.bam.flagstat",
+            "WT_REP1.sorted.bam.idxstats",
+            "WT_REP1.sorted.bam.stats",
+            "WT_REP2.markdup.sorted.bam.flagstat",
+            "WT_REP2.markdup.sorted.bam.idxstats",
+            "WT_REP2.markdup.sorted.bam.stats",
+            "WT_REP2.sorted.bam.flagstat",
+            "WT_REP2.sorted.bam.idxstats",
+            "WT_REP2.sorted.bam.stats"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T18:42:17.143005"
+    },
+    "Params: default - stub": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}",
+            "genome_transcriptome.fasta",
+            "genome_transcriptome.gtf",
+            "RAP1_IAA_30M_REP1_raw.html",
+            "RAP1_IAA_30M_REP1_raw.zip",
+            "RAP1_UNINDUCED_REP1_raw.html",
+            "RAP1_UNINDUCED_REP1_raw.zip",
+            "RAP1_UNINDUCED_REP2_raw.html",
+            "RAP1_UNINDUCED_REP2_raw.zip",
+            "WT_REP1_raw.html",
+            "WT_REP1_raw.zip",
+            "WT_REP2_raw.html",
+            "WT_REP2_raw.zip",
+            "multiqc_report.html",
+            "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T14:00:48.949429"
+    },
+    "multiqc_plots": {
+        "content": [
+            "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
+            "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
+            "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
+            "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6",
+            "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890",
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+            "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f",
+            "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14",
+            "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
+            "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959",
+            "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16",
+            "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881",
+            "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e",
+            "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb",
+            "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
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+    "star_salmon/qualimap": {
+        "content": [
+            "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d",
+            "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4",
+            "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a",
+            "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37",
+            "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8",
+            "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
+            "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
+            "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518",
+            "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d",
+            "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50",
+            "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe",
+            "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3",
+            "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff",
+            "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff",
+            "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58",
+            "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90",
+            "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8",
+            "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518",
+            "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e",
+            "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d",
+            "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d",
+            "Coverage Profile Along Genes (High).png:md5,c974d47996bcc57b99dfaf6903f61f41",
+            "Coverage Profile Along Genes (Low).png:md5,c8fe631f0580c93adb5be107c6a7a1a3",
+            "Coverage Profile Along Genes (Total).png:md5,424d245e9f3e626d9e79f51d1b93e946",
+            "Transcript coverage histogram.png:md5,17404146ad5e0a9bce97ce622e00975e",
+            "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1",
+            "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211",
+            "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211",
+            "Coverage Profile Along Genes (High).png:md5,40edd79c21f3e8d8bbac384156c472d6",
+            "Coverage Profile Along Genes (Low).png:md5,935c0372259a953a4c99569e9b236ae5",
+            "Coverage Profile Along Genes (Total).png:md5,34f7a4307be1ea674b7b98eee564d96b",
+            "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d",
+            "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3",
+            "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b",
+            "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:44:57.740534"
+    }
+}
\ No newline at end of file
diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test
new file mode 100644
index 000000000..16794293b
--- /dev/null
+++ b/tests/featurecounts_group_type.nf.test
@@ -0,0 +1,933 @@
+nextflow_pipeline {
+
+    name "Test pipeline without a group type for featureCounts"
+    script "../main.nf"
+
+    test("Params: --featurecounts_group_type false") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                featurecounts_group_type = false
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name
+                ).match("fastqc/raw") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name
+                ).match("fastqc/trim") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name
+                ).match("salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.sf").name
+                ).match("salmon_quant") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name
+                ).match("star_salmon/bigwig") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name
+                ).match("star_salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"),
+                    // PDFs are not stable
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name
+                ).match("star_salmon/dupradar") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"),
+                    // Logs are not stable
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name
+                ).match("star_salmon/log") },
+                { assert snapshot(
+                    // Metrics are not stable
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name
+                ).match("star_salmon/picard_metrics") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    // HTML reports and these files are not stable
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name
+                ).match("star_salmon/qualimap") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"),
+                    // PDFs, R scripts and all these files are not stable
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name
+                ).match("star_salmon/rseqc") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("star_salmon/salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name
+                ).match("star_salmon/samtools_stats") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name
+                ).match("star_salmon/stringtie") },
+                { assert snapshot(
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name
+                ).match("star_salmon/markdup") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name
+                ).match("star_salmon/salmon_quant") },
+                { assert snapshot(
+                    // These reports are not stable
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match("trimgalore") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    test("Params: --featurecounts_group_type false - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                featurecounts_group_type = false
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    file("${params.outdir}/custom/out/genome_transcriptome.fasta").name,
+                    file("${params.outdir}/custom/out/genome_transcriptome.gtf").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
new file mode 100644
index 000000000..a7e6910dd
--- /dev/null
+++ b/tests/featurecounts_group_type.nf.test.snap
@@ -0,0 +1,1044 @@
+{
+    "star_salmon/log": {
+        "content": [
+            "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee",
+            "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8",
+            "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
+            "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204",
+            "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23",
+            "RAP1_IAA_30M_REP1.Log.final.out",
+            "RAP1_IAA_30M_REP1.Log.out",
+            "RAP1_IAA_30M_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP1.Log.final.out",
+            "RAP1_UNINDUCED_REP1.Log.out",
+            "RAP1_UNINDUCED_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP2.Log.final.out",
+            "RAP1_UNINDUCED_REP2.Log.out",
+            "RAP1_UNINDUCED_REP2.Log.progress.out",
+            "WT_REP1.Log.final.out",
+            "WT_REP1.Log.out",
+            "WT_REP1.Log.progress.out",
+            "WT_REP2.Log.final.out",
+            "WT_REP2.Log.out",
+            "WT_REP2.Log.progress.out"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T17:43:26.652121"
+    },
+    "star_salmon/salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020",
+            "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5",
+            "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748",
+            "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde",
+            "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae",
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T13:34:18.439694"
+    },
+    "multiqc_data": {
+        "content": [
+            "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+            "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
+            "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+            "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+            "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+            "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+            "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+            "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e",
+            "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+            "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
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+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,041edee3193df311f621c09f4991892b",
+            "t_data.ctab",
+            "RAP1_IAA_30M_REP1.coverage.gtf",
+            "RAP1_IAA_30M_REP1.gene.abundance.txt",
+            "RAP1_IAA_30M_REP1.transcripts.gtf",
+            "t_data.ctab",
+            "RAP1_UNINDUCED_REP1.coverage.gtf",
+            "RAP1_UNINDUCED_REP1.gene.abundance.txt",
+            "RAP1_UNINDUCED_REP1.transcripts.gtf",
+            "t_data.ctab",
+            "RAP1_UNINDUCED_REP2.coverage.gtf",
+            "RAP1_UNINDUCED_REP2.gene.abundance.txt",
+            "RAP1_UNINDUCED_REP2.transcripts.gtf",
+            "t_data.ctab",
+            "WT_REP1.coverage.gtf",
+            "WT_REP1.gene.abundance.txt",
+            "WT_REP1.transcripts.gtf",
+            "t_data.ctab",
+            "WT_REP2.coverage.gtf",
+            "WT_REP2.gene.abundance.txt",
+            "WT_REP2.transcripts.gtf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T17:43:26.873868"
+    },
+    "fastqc/trim": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip",
+            "WT_REP1_trimmed_1_val_1_fastqc.html",
+            "WT_REP1_trimmed_1_val_1_fastqc.zip",
+            "WT_REP1_trimmed_2_val_2_fastqc.html",
+            "WT_REP1_trimmed_2_val_2_fastqc.zip",
+            "WT_REP2_trimmed_1_val_1_fastqc.html",
+            "WT_REP2_trimmed_1_val_1_fastqc.zip",
+            "WT_REP2_trimmed_2_val_2_fastqc.html",
+            "WT_REP2_trimmed_2_val_2_fastqc.zip"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T15:44:10.142955"
+    },
+    "star_salmon/dupradar": {
+        "content": [
+            "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217",
+            "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370",
+            "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b",
+            "WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00",
+            "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5",
+            "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
+            "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
+            "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
+            "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef",
+            "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e",
+            "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf",
+            "WT_REP1_duprateExpBoxplot.pdf",
+            "WT_REP2_duprateExpBoxplot.pdf",
+            "RAP1_IAA_30M_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP2_expressionHist.pdf",
+            "WT_REP1_expressionHist.pdf",
+            "WT_REP2_expressionHist.pdf",
+            "RAP1_IAA_30M_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpDens.pdf",
+            "WT_REP1_duprateExpDens.pdf",
+            "WT_REP2_duprateExpDens.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T17:34:58.606096"
+    },
+    "bbsplit": {
+        "content": [
+            "RAP1_IAA_30M_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP2.stats.txt",
+            "WT_REP1.stats.txt",
+            "WT_REP2.stats.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T16:30:34.908301"
+    },
+    "salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c",
+            "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1",
+            "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636",
+            "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935",
+            "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326",
+            "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3",
+            "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d",
+            "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6",
+            "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac",
+            "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T17:34:58.29814"
+    },
+    "star_salmon/qualimap": {
+        "content": [
+            "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d",
+            "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4",
+            "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a",
+            "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37",
+            "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8",
+            "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
+            "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
+            "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518",
+            "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d",
+            "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50",
+            "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe",
+            "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3",
+            "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff",
+            "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff",
+            "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58",
+            "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90",
+            "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8",
+            "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518",
+            "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e",
+            "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d",
+            "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d",
+            "Coverage Profile Along Genes (High).png:md5,c974d47996bcc57b99dfaf6903f61f41",
+            "Coverage Profile Along Genes (Low).png:md5,c8fe631f0580c93adb5be107c6a7a1a3",
+            "Coverage Profile Along Genes (Total).png:md5,424d245e9f3e626d9e79f51d1b93e946",
+            "Transcript coverage histogram.png:md5,17404146ad5e0a9bce97ce622e00975e",
+            "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1",
+            "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211",
+            "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211",
+            "Coverage Profile Along Genes (High).png:md5,40edd79c21f3e8d8bbac384156c472d6",
+            "Coverage Profile Along Genes (Low).png:md5,935c0372259a953a4c99569e9b236ae5",
+            "Coverage Profile Along Genes (Total).png:md5,34f7a4307be1ea674b7b98eee564d96b",
+            "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d",
+            "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3",
+            "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b",
+            "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T14:18:38.410297"
+    }
+}
\ No newline at end of file
diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test
new file mode 100644
index 000000000..9577086ea
--- /dev/null
+++ b/tests/hisat2.nf.test
@@ -0,0 +1,861 @@
+nextflow_pipeline {
+
+    name "Test pipeline with HISAT2 aligner"
+    script "../main.nf"
+
+    test("Params: --aligner hisat2") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = 'hisat2'
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name
+                ).match("fastqc/raw") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name
+                ).match("fastqc/trim") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name,
+                    file("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name,
+                    file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name,
+                    file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name,
+                    file("${params.outdir}/hisat2/bigwig/WT_REP1.forward.bigWig").name,
+                    file("${params.outdir}/hisat2/bigwig/WT_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/hisat2/bigwig/WT_REP2.forward.bigWig").name,
+                    file("${params.outdir}/hisat2/bigwig/WT_REP2.reverse.bigWig").name
+                ).match("hisat2/bigwig") },
+                { assert snapshot(
+                    path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/hisat2/dupradar/gene_data/WT_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/hisat2/dupradar/gene_data/WT_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/hisat2/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/hisat2/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/hisat2/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"),
+                    path("${params.outdir}/hisat2/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/hisat2/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"),
+                    // PDFs are not stable
+                    file("${params.outdir}/hisat2/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/histogram/WT_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/histogram/WT_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/hisat2/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name
+                ).match("hisat2/dupradar") },
+                { assert snapshot(
+                    path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"),
+                    path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"),
+                    path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"),
+                    path("${params.outdir}/hisat2/featurecounts/WT_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/WT_REP1.featureCounts.txt"),
+                    path("${params.outdir}/hisat2/featurecounts/WT_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt"),
+                    file("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name,
+                    file("${params.outdir}/hisat2/featurecounts/WT_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt.summary").name
+                ).match("hisat2/featurecounts") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/hisat2/RAP1_IAA_30M_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/hisat2/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/hisat2/WT_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/hisat2/WT_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/hisat2/WT_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/hisat2/WT_REP2.markdup.sorted.bam.bai").name
+                ).match("hisat2/markdup") },
+                { assert snapshot(
+                    file("${params.outdir}/hisat2/log/RAP1_IAA_30M_REP1.hisat2.summary.log").name,
+                    file("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP1.hisat2.summary.log").name,
+                    file("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP2.hisat2.summary.log").name,
+                    file("${params.outdir}/hisat2/log/WT_REP1.hisat2.summary.log").name,
+                    file("${params.outdir}/hisat2/log/WT_REP2.hisat2.summary.log").name
+                ).match("hisat2") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_filtered_reads_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap-1.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_adapter_content_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_cutadapt.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_idxstats.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram_1.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram_2.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_infer_experiment_plot.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/junction_saturation_known.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/junction_saturation_novel.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_dupradar-section-plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fail_strand_check_table.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_picard_dups.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_flagstat.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_sources.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_deduplication.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_all.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_distribution_plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_dups.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_dups_plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/salmon_plot.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-stats-dp.txt").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools_alignment_plot.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/dupradar-section-plot.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_dups_plot.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/general_stats_table.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/salmon_plot.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fail_strand_check_table.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/general_stats_table.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-cnt.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-pct.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_bam_stat.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_plot.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-stats-dp.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/dupradar-section-plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fail_strand_check_table.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/general_stats_table.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/picard_deduplication-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_bam_stat.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/salmon_plot.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-stats-dp.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    // Metrics are not stable
+                    file("${params.outdir}/hisat2/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/hisat2/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/hisat2/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/hisat2/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/hisat2/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name
+                ).match("hisat2/picard_metrics") },
+                { assert snapshot(
+                    path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    // HTML reports and these files are not stable
+                    file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/hisat2/qualimap/WT_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/hisat2/qualimap/WT_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/hisat2/qualimap/WT_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/hisat2/qualimap/WT_REP2/rnaseq_qc_results.txt").name
+                ).match("hisat2/qualimap") },
+                { assert snapshot(
+                    path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"),
+                    path("${params.outdir}/hisat2/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/hisat2/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"),
+                    // PDFs, R scripts and all these files are not stable
+                    file("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name
+                ).match("hisat2/rseqc") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.stats").name
+                ).match("hisat2/samtools_stats") },
+                { assert snapshot(
+                    path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/i_data.ctab"),
+                    // These files are not stable
+                    file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name,
+                    file("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/hisat2/stringtie/WT_REP1.coverage.gtf").name,
+                    file("${params.outdir}/hisat2/stringtie/WT_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/hisat2/stringtie/WT_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/hisat2/stringtie/WT_REP2.coverage.gtf").name,
+                    file("${params.outdir}/hisat2/stringtie/WT_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/hisat2/stringtie/WT_REP2.transcripts.gtf").name
+                ).match("hisat2/stringtie") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name
+                ).match("salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.sf").name
+                ).match("salmon_quant") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("salmon") },
+                { assert snapshot(
+                    // These reports are not stable
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match("trimgalore") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    test("Params: --aligner hisat2 - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = 'hisat2'
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    file("${params.outdir}/custom/out/genome_transcriptome.fasta").name,
+                    file("${params.outdir}/custom/out/genome_transcriptome.gtf").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name,
+                    file("${params.outdir}/multiqc/hisat2/multiqc_report.html").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
new file mode 100644
index 000000000..db5ac14e1
--- /dev/null
+++ b/tests/hisat2.nf.test.snap
@@ -0,0 +1,961 @@
+{
+    "hisat2/rseqc": {
+        "content": [
+            "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1d4348685fa61819ff8076213d0873b3",
+            "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,3ee0f64e82f0b1ac16b5f3e2b30b024c",
+            "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,3d17628d178e5a3cc9dc03f32614bff7",
+            "WT_REP1.infer_experiment.txt:md5,13e3c748f5b968455a39eb9fefd87053",
+            "WT_REP2.infer_experiment.txt:md5,230910b354a5531d1c4bf711ccd6e493",
+            "RAP1_IAA_30M_REP1.bam_stat.txt",
+            "RAP1_UNINDUCED_REP1.bam_stat.txt",
+            "RAP1_UNINDUCED_REP2.bam_stat.txt",
+            "WT_REP1.bam_stat.txt",
+            "WT_REP2.bam_stat.txt",
+            "RAP1_IAA_30M_REP1.inner_distance_plot.pdf",
+            "WT_REP1.inner_distance_plot.pdf",
+            "WT_REP2.inner_distance_plot.pdf",
+            "RAP1_IAA_30M_REP1.inner_distance_plot.r",
+            "WT_REP1.inner_distance_plot.r",
+            "WT_REP2.inner_distance_plot.r",
+            "RAP1_IAA_30M_REP1.inner_distance.txt",
+            "RAP1_IAA_30M_REP1.inner_distance_freq.txt",
+            "RAP1_IAA_30M_REP1.inner_distance_mean.txt",
+            "WT_REP1.inner_distance.txt",
+            "WT_REP1.inner_distance_freq.txt",
+            "WT_REP1.inner_distance_mean.txt",
+            "WT_REP2.inner_distance.txt",
+            "WT_REP2.inner_distance_freq.txt",
+            "WT_REP2.inner_distance_mean.txt",
+            "RAP1_IAA_30M_REP1.junction.Interact.bed",
+            "RAP1_IAA_30M_REP1.junction.bed",
+            "RAP1_UNINDUCED_REP1.junction.Interact.bed",
+            "RAP1_UNINDUCED_REP1.junction.bed",
+            "RAP1_UNINDUCED_REP2.junction.Interact.bed",
+            "RAP1_UNINDUCED_REP2.junction.bed",
+            "WT_REP1.junction.Interact.bed",
+            "WT_REP1.junction.bed",
+            "WT_REP2.junction.Interact.bed",
+            "WT_REP2.junction.bed",
+            "RAP1_IAA_30M_REP1.junction_annotation.log",
+            "RAP1_UNINDUCED_REP1.junction_annotation.log",
+            "RAP1_UNINDUCED_REP2.junction_annotation.log",
+            "WT_REP1.junction_annotation.log",
+            "WT_REP2.junction_annotation.log",
+            "RAP1_IAA_30M_REP1.splice_events.pdf",
+            "RAP1_IAA_30M_REP1.splice_junction.pdf",
+            "RAP1_UNINDUCED_REP1.splice_events.pdf",
+            "RAP1_UNINDUCED_REP1.splice_junction.pdf",
+            "RAP1_UNINDUCED_REP2.splice_events.pdf",
+            "RAP1_UNINDUCED_REP2.splice_junction.pdf",
+            "WT_REP1.splice_events.pdf",
+            "WT_REP1.splice_junction.pdf",
+            "WT_REP2.splice_events.pdf",
+            "WT_REP2.splice_junction.pdf",
+            "RAP1_IAA_30M_REP1.junction_plot.r",
+            "RAP1_UNINDUCED_REP1.junction_plot.r",
+            "RAP1_UNINDUCED_REP2.junction_plot.r",
+            "WT_REP1.junction_plot.r",
+            "WT_REP2.junction_plot.r",
+            "RAP1_IAA_30M_REP1.junction.xls",
+            "RAP1_UNINDUCED_REP1.junction.xls",
+            "RAP1_UNINDUCED_REP2.junction.xls",
+            "WT_REP1.junction.xls",
+            "WT_REP2.junction.xls",
+            "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf",
+            "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf",
+            "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf",
+            "WT_REP1.junctionSaturation_plot.pdf",
+            "WT_REP2.junctionSaturation_plot.pdf",
+            "RAP1_IAA_30M_REP1.junctionSaturation_plot.r",
+            "RAP1_UNINDUCED_REP1.junctionSaturation_plot.r",
+            "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r",
+            "WT_REP1.junctionSaturation_plot.r",
+            "WT_REP2.junctionSaturation_plot.r",
+            "RAP1_IAA_30M_REP1.read_distribution.txt",
+            "RAP1_UNINDUCED_REP1.read_distribution.txt",
+            "RAP1_UNINDUCED_REP2.read_distribution.txt",
+            "WT_REP1.read_distribution.txt",
+            "WT_REP2.read_distribution.txt",
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+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip",
+            "WT_REP1_trimmed_1_val_1_fastqc.html",
+            "WT_REP1_trimmed_1_val_1_fastqc.zip",
+            "WT_REP1_trimmed_2_val_2_fastqc.html",
+            "WT_REP1_trimmed_2_val_2_fastqc.zip",
+            "WT_REP2_trimmed_1_val_1_fastqc.html",
+            "WT_REP2_trimmed_1_val_1_fastqc.zip",
+            "WT_REP2_trimmed_2_val_2_fastqc.html",
+            "WT_REP2_trimmed_2_val_2_fastqc.zip"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T12:35:11.679664"
+    },
+    "hisat2/dupradar": {
+        "content": [
+            "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8a6bf324a928534cb7ed7a5522aff7d0",
+            "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,ae3e70edc98ec8117608f8f608effab9",
+            "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,9a5c2672c5817e930c7b884ada8fd92c",
+            "WT_REP1_dupMatrix.txt:md5,11371da7a087879340c2e7e6842a5d89",
+            "WT_REP2_dupMatrix.txt:md5,5176c7447c4295f94e2683dd9995cea0",
+            "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,1285c70833b46849b726412858736ed7",
+            "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a2efe7c3cad6f910d5dc208c2825a245",
+            "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,117712525fcbd396f77710f4f4b605d9",
+            "WT_REP1_intercept_slope.txt:md5,df33cbc6c3cb1c85c0c06cdba7df3873",
+            "WT_REP2_intercept_slope.txt:md5,38fbb93a419e666bc81020602852b1e2",
+            "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf",
+            "WT_REP1_duprateExpBoxplot.pdf",
+            "WT_REP2_duprateExpBoxplot.pdf",
+            "RAP1_IAA_30M_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP2_expressionHist.pdf",
+            "WT_REP1_expressionHist.pdf",
+            "WT_REP2_expressionHist.pdf",
+            "RAP1_IAA_30M_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpDens.pdf",
+            "WT_REP1_duprateExpDens.pdf",
+            "WT_REP2_duprateExpDens.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T12:35:11.695025"
+    },
+    "hisat2": {
+        "content": [
+            "RAP1_IAA_30M_REP1.hisat2.summary.log",
+            "RAP1_UNINDUCED_REP1.hisat2.summary.log",
+            "RAP1_UNINDUCED_REP2.hisat2.summary.log",
+            "WT_REP1.hisat2.summary.log",
+            "WT_REP2.hisat2.summary.log"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T13:40:29.865928"
+    },
+    "hisat2/stringtie": {
+        "content": [
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,c93ce5b90352398208e3d88c68df45c6",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,fe9d92d1d28e1bc1b223e2ce22b4ef05",
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,293d64f70bd8353b822e4fa8a6f082a3",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a",
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,ed48a29b77c315cb61a6bf09e68c877d",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,cf2506824949c02e0bfde17a9ed86e61",
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,a17c7749a005a89875876eb2d90721d4",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,2e2d760739539fba09cbb666ab95afa1",
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,22bdc84c1c4acce9798868e8c7b56004",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,80fe14762a8f7230d516bba37b7275d1",
+            "t_data.ctab",
+            "RAP1_IAA_30M_REP1.coverage.gtf",
+            "RAP1_IAA_30M_REP1.gene.abundance.txt",
+            "RAP1_IAA_30M_REP1.transcripts.gtf",
+            "t_data.ctab",
+            "RAP1_UNINDUCED_REP1.coverage.gtf",
+            "RAP1_UNINDUCED_REP1.gene.abundance.txt",
+            "RAP1_UNINDUCED_REP1.transcripts.gtf",
+            "t_data.ctab",
+            "RAP1_UNINDUCED_REP2.coverage.gtf",
+            "RAP1_UNINDUCED_REP2.gene.abundance.txt",
+            "RAP1_UNINDUCED_REP2.transcripts.gtf",
+            "t_data.ctab",
+            "WT_REP1.coverage.gtf",
+            "WT_REP1.gene.abundance.txt",
+            "WT_REP1.transcripts.gtf",
+            "t_data.ctab",
+            "WT_REP2.coverage.gtf",
+            "WT_REP2.gene.abundance.txt",
+            "WT_REP2.transcripts.gtf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T12:35:11.865423"
+    },
+    "bbsplit": {
+        "content": [
+            "RAP1_IAA_30M_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP2.stats.txt",
+            "WT_REP1.stats.txt",
+            "WT_REP2.stats.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T10:32:15.589105"
+    },
+    "salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c",
+            "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1",
+            "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636",
+            "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935",
+            "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326",
+            "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3",
+            "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d",
+            "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6",
+            "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac",
+            "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T12:35:11.954394"
+    },
+    "hisat2/markdup": {
+        "content": [
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam",
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai",
+            "WT_REP1.markdup.sorted.bam",
+            "WT_REP1.markdup.sorted.bam.bai",
+            "WT_REP2.markdup.sorted.bam",
+            "WT_REP2.markdup.sorted.bam.bai"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T13:40:29.820359"
+    }
+}
\ No newline at end of file
diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test
new file mode 100644
index 000000000..7343798f7
--- /dev/null
+++ b/tests/kallisto.nf.test
@@ -0,0 +1,225 @@
+nextflow_pipeline {
+
+    name "Test pipeline with Kallisto, skipping both QC and alignment"
+    script "../main.nf"
+
+    test("Params: --pseudo_aligner kallisto --skip_qc --skip_alignment") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                pseudo_aligner = 'kallisto'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name
+                ).match("fastqc/trim") },
+                { assert snapshot(
+                    path("${params.outdir}/kallisto/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.h5").name,
+                    file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.tsv").name,
+                    file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/kallisto_quant.log").name,
+                    file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/run_info.json").name,
+                    file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.h5").name,
+                    file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.tsv").name,
+                    file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/kallisto_quant.log").name,
+                    file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/run_info.json").name,
+                    file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.h5").name,
+                    file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.tsv").name,
+                    file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/kallisto_quant.log").name,
+                    file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/run_info.json").name,
+                    file("${params.outdir}/kallisto/WT_REP1/abundance.h5").name,
+                    file("${params.outdir}/kallisto/WT_REP1/abundance.tsv").name,
+                    file("${params.outdir}/kallisto/WT_REP1/kallisto_quant.log").name,
+                    file("${params.outdir}/kallisto/WT_REP1/run_info.json").name,
+                    file("${params.outdir}/kallisto/WT_REP2/abundance.h5").name,
+                    file("${params.outdir}/kallisto/WT_REP2/abundance.tsv").name,
+                    file("${params.outdir}/kallisto/WT_REP2/kallisto_quant.log").name,
+                    file("${params.outdir}/kallisto/WT_REP2/run_info.json").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/kallisto/kallisto.merged.transcript_tpm.tsv").name
+                ).match("kallisto") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/multiqc_cutadapt.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/kallisto_alignment.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_kallisto.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_sources.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/general_stats_table.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-pct.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/general_stats_table.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-cnt.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-pct.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/general_stats_table.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-cnt.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-pct.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    // These reports are not stable
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match("trimgalore") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    test("Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                pseudo_aligner = 'kallisto'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    file("${params.outdir}/custom/out/genome_transcriptome.fasta").name,
+                    file("${params.outdir}/custom/out/genome_transcriptome.gtf").name,
+                    file("${params.outdir}/multiqc/multiqc_report.html").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
new file mode 100644
index 000000000..809f4e0f2
--- /dev/null
+++ b/tests/kallisto.nf.test.snap
@@ -0,0 +1,241 @@
+{
+    "multiqc_data": {
+        "content": [
+            "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+            "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
+            "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+            "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+            "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+            "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+            "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+            "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+            "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+            "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c",
+            "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
+            "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+            "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee",
+            "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
+            "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+            "fastqc_top_overrepresented_sequences_table.txt",
+            "kallisto_alignment.txt",
+            "multiqc_data.json",
+            "multiqc_general_stats.txt",
+            "multiqc_kallisto.txt",
+            "multiqc_software_versions.txt",
+            "multiqc_sources.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:53:37.272547"
+    },
+    "trimgalore": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:35:31.545385"
+    },
+    "kallisto": {
+        "content": [
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "kallisto.merged.gene_counts.SummarizedExperiment.rds",
+            "kallisto.merged.gene_counts.tsv",
+            "kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds",
+            "kallisto.merged.gene_counts_length_scaled.tsv",
+            "kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds",
+            "kallisto.merged.gene_counts_scaled.tsv",
+            "kallisto.merged.gene_lengths.tsv",
+            "kallisto.merged.gene_tpm.tsv",
+            "kallisto.merged.transcript_counts.SummarizedExperiment.rds",
+            "kallisto.merged.transcript_counts.tsv",
+            "kallisto.merged.transcript_lengths.tsv",
+            "kallisto.merged.transcript_tpm.tsv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:53:37.166056"
+    },
+    "references": {
+        "content": [
+            "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
+            "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:25:12.683541"
+    },
+    "versions": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:35:31.742801"
+    },
+    "fastqc/trim": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip",
+            "WT_REP1_trimmed_1_val_1_fastqc.html",
+            "WT_REP1_trimmed_1_val_1_fastqc.zip",
+            "WT_REP1_trimmed_2_val_2_fastqc.html",
+            "WT_REP1_trimmed_2_val_2_fastqc.zip",
+            "WT_REP2_trimmed_1_val_1_fastqc.html",
+            "WT_REP2_trimmed_1_val_1_fastqc.zip",
+            "WT_REP2_trimmed_2_val_2_fastqc.html",
+            "WT_REP2_trimmed_2_val_2_fastqc.zip"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:25:12.695474"
+    },
+    "multiqc_plots": {
+        "content": [
+            "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
+            "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
+            "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
+            "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890",
+            "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f",
+            "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
+            "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959",
+            "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e",
+            "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
+            "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
+            "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
+            "multiqc_report.html",
+            "cutadapt_filtered_reads_plot-cnt.pdf",
+            "cutadapt_filtered_reads_plot-pct.pdf",
+            "cutadapt_trimmed_sequences_plot_3_Counts.pdf",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
+            "fastqc-status-check-heatmap.pdf",
+            "fastqc_overrepresented_sequences_plot.pdf",
+            "fastqc_per_base_n_content_plot.pdf",
+            "fastqc_per_base_sequence_quality_plot.pdf",
+            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+            "fastqc_per_sequence_quality_scores_plot.pdf",
+            "fastqc_sequence_counts_plot-cnt.pdf",
+            "fastqc_sequence_counts_plot-pct.pdf",
+            "fastqc_sequence_duplication_levels_plot.pdf",
+            "fastqc_sequence_length_distribution_plot.pdf",
+            "fastqc_top_overrepresented_sequences_table.pdf",
+            "general_stats_table.pdf",
+            "kallisto_alignment-cnt.pdf",
+            "kallisto_alignment-pct.pdf",
+            "fastqc_per_base_n_content_plot.png",
+            "fastqc_per_base_sequence_quality_plot.png",
+            "fastqc_sequence_length_distribution_plot.png",
+            "fastqc_top_overrepresented_sequences_table.png",
+            "general_stats_table.png",
+            "kallisto_alignment-cnt.png",
+            "kallisto_alignment-pct.png",
+            "cutadapt_filtered_reads_plot-cnt.svg",
+            "cutadapt_filtered_reads_plot-pct.svg",
+            "cutadapt_trimmed_sequences_plot_3_Counts.svg",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
+            "fastqc-status-check-heatmap.svg",
+            "fastqc_overrepresented_sequences_plot.svg",
+            "fastqc_per_base_n_content_plot.svg",
+            "fastqc_per_base_sequence_quality_plot.svg",
+            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+            "fastqc_per_sequence_quality_scores_plot.svg",
+            "fastqc_sequence_counts_plot-cnt.svg",
+            "fastqc_sequence_counts_plot-pct.svg",
+            "fastqc_sequence_duplication_levels_plot.svg",
+            "fastqc_sequence_length_distribution_plot.svg",
+            "fastqc_top_overrepresented_sequences_table.svg",
+            "general_stats_table.svg",
+            "kallisto_alignment-cnt.svg",
+            "kallisto_alignment-pct.svg"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:53:37.413284"
+    },
+    "bbsplit": {
+        "content": [
+            "RAP1_IAA_30M_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP2.stats.txt",
+            "WT_REP1.stats.txt",
+            "WT_REP2.stats.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:25:12.672876"
+    },
+    "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}",
+            "genome_transcriptome.fasta",
+            "genome_transcriptome.gtf",
+            "multiqc_report.html",
+            "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:36:19.174739"
+    }
+}
\ No newline at end of file
diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy
new file mode 100644
index 000000000..1bd58a496
--- /dev/null
+++ b/tests/lib/UTILS.groovy
@@ -0,0 +1,11 @@
+// Function to remove Nextflow version from pipeline_software_mqc_versions.yml
+
+class UTILS {
+    public static String removeNextflowVersion(pipeline_software_mqc_versions) {
+        def softwareVersions = path(pipeline_software_mqc_versions).yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+}
diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test
new file mode 100644
index 000000000..dde1c3706
--- /dev/null
+++ b/tests/min_mapped_reads.nf.test
@@ -0,0 +1,852 @@
+nextflow_pipeline {
+
+    name "Test pipeline with a minimum mapped read threshold of 90"
+    script "../main.nf"
+
+    test("Params: --min_mapped_reads 90") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                min_mapped_reads = 90
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name
+                ).match("fastqc/raw") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name
+                ).match("fastqc/trim") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_mapped_samples_table.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_mapped_samples_table.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_mapped_samples_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_mapped_samples_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name
+                ).match("salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.sf").name
+                ).match("salmon_quant") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name
+                ).match("star_salmon/bigwig") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name
+                ).match("star_salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"),
+                    // PDFs are not stable
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name
+                ).match("star_salmon/dupradar") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"),
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name
+                ).match("star_salmon/featurecounts") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"),
+                    // Logs are not stable
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name
+                ).match("star_salmon/log") },
+                { assert snapshot(
+                    // Metrics are not stable
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name
+                ).match("star_salmon/picard_metrics") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    // HTML reports and these files are not stable
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name
+                ).match("star_salmon/qualimap") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"),
+                    // PDFs, R scripts and all these files are not stable
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name
+                ).match("star_salmon/rseqc") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("star_salmon/salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name
+                ).match("star_salmon/samtools_stats") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name
+                ).match("star_salmon/stringtie") },
+                { assert snapshot(
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name
+                ).match("star_salmon/markdup") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name
+                ).match("star_salmon/salmon_quant") },
+                { assert snapshot(
+                    // These reports are not stable
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match("trimgalore") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    test("Params: --min_mapped_reads 90 - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                min_mapped_reads = 90
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    file("${params.outdir}/custom/out/genome_transcriptome.fasta").name,
+                    file("${params.outdir}/custom/out/genome_transcriptome.gtf").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
new file mode 100644
index 000000000..941a21a58
--- /dev/null
+++ b/tests/min_mapped_reads.nf.test.snap
@@ -0,0 +1,970 @@
+{
+    "star_salmon/log": {
+        "content": [
+            "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee",
+            "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8",
+            "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
+            "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204",
+            "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23",
+            "RAP1_IAA_30M_REP1.Log.final.out",
+            "RAP1_IAA_30M_REP1.Log.out",
+            "RAP1_IAA_30M_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP1.Log.final.out",
+            "RAP1_UNINDUCED_REP1.Log.out",
+            "RAP1_UNINDUCED_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP2.Log.final.out",
+            "RAP1_UNINDUCED_REP2.Log.out",
+            "RAP1_UNINDUCED_REP2.Log.progress.out",
+            "WT_REP1.Log.final.out",
+            "WT_REP1.Log.out",
+            "WT_REP1.Log.progress.out",
+            "WT_REP2.Log.final.out",
+            "WT_REP2.Log.out",
+            "WT_REP2.Log.progress.out"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:36:12.254374"
+    },
+    "star_salmon/salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020",
+            "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5",
+            "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748",
+            "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde",
+            "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae",
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:36:12.647521"
+    },
+    "trimgalore": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:36:12.719201"
+    },
+    "star_salmon/rseqc": {
+        "content": [
+            "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33",
+            "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,2ca0ce0fd3204bd2cc4812c4655b1f1f",
+            "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40",
+            "RAP1_IAA_30M_REP1.bam_stat.txt",
+            "RAP1_UNINDUCED_REP1.bam_stat.txt",
+            "RAP1_UNINDUCED_REP2.bam_stat.txt",
+            "RAP1_IAA_30M_REP1.inner_distance_plot.pdf",
+            "RAP1_IAA_30M_REP1.inner_distance_plot.r",
+            "RAP1_IAA_30M_REP1.inner_distance.txt",
+            "RAP1_IAA_30M_REP1.inner_distance_freq.txt",
+            "RAP1_IAA_30M_REP1.inner_distance_mean.txt",
+            "RAP1_IAA_30M_REP1.junction.Interact.bed",
+            "RAP1_IAA_30M_REP1.junction.bed",
+            "RAP1_UNINDUCED_REP1.junction.Interact.bed",
+            "RAP1_UNINDUCED_REP1.junction.bed",
+            "RAP1_UNINDUCED_REP2.junction.Interact.bed",
+            "RAP1_UNINDUCED_REP2.junction.bed",
+            "RAP1_IAA_30M_REP1.junction_annotation.log",
+            "RAP1_UNINDUCED_REP1.junction_annotation.log",
+            "RAP1_UNINDUCED_REP2.junction_annotation.log",
+            "RAP1_IAA_30M_REP1.splice_events.pdf",
+            "RAP1_IAA_30M_REP1.splice_junction.pdf",
+            "RAP1_UNINDUCED_REP1.splice_events.pdf",
+            "RAP1_UNINDUCED_REP1.splice_junction.pdf",
+            "RAP1_UNINDUCED_REP2.splice_events.pdf",
+            "RAP1_UNINDUCED_REP2.splice_junction.pdf",
+            "RAP1_IAA_30M_REP1.junction_plot.r",
+            "RAP1_UNINDUCED_REP1.junction_plot.r",
+            "RAP1_UNINDUCED_REP2.junction_plot.r",
+            "RAP1_IAA_30M_REP1.junction.xls",
+            "RAP1_UNINDUCED_REP1.junction.xls",
+            "RAP1_UNINDUCED_REP2.junction.xls",
+            "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf",
+            "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf",
+            "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf",
+            "RAP1_IAA_30M_REP1.junctionSaturation_plot.r",
+            "RAP1_UNINDUCED_REP1.junctionSaturation_plot.r",
+            "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r",
+            "RAP1_IAA_30M_REP1.read_distribution.txt",
+            "RAP1_UNINDUCED_REP1.read_distribution.txt",
+            "RAP1_UNINDUCED_REP2.read_distribution.txt",
+            "RAP1_IAA_30M_REP1.DupRate_plot.pdf",
+            "RAP1_UNINDUCED_REP1.DupRate_plot.pdf",
+            "RAP1_UNINDUCED_REP2.DupRate_plot.pdf",
+            "RAP1_IAA_30M_REP1.DupRate_plot.r",
+            "RAP1_UNINDUCED_REP1.DupRate_plot.r",
+            "RAP1_UNINDUCED_REP2.DupRate_plot.r",
+            "RAP1_IAA_30M_REP1.pos.DupRate.xls",
+            "RAP1_IAA_30M_REP1.seq.DupRate.xls",
+            "RAP1_UNINDUCED_REP1.pos.DupRate.xls",
+            "RAP1_UNINDUCED_REP1.seq.DupRate.xls",
+            "RAP1_UNINDUCED_REP2.pos.DupRate.xls",
+            "RAP1_UNINDUCED_REP2.seq.DupRate.xls"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:06:37.124481"
+    },
+    "references": {
+        "content": [
+            "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
+            "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:04:54.733969"
+    },
+    "star_salmon/samtools_stats": {
+        "content": [
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat",
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats",
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats",
+            "RAP1_IAA_30M_REP1.sorted.bam.flagstat",
+            "RAP1_IAA_30M_REP1.sorted.bam.idxstats",
+            "RAP1_IAA_30M_REP1.sorted.bam.stats",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats",
+            "RAP1_UNINDUCED_REP1.sorted.bam.flagstat",
+            "RAP1_UNINDUCED_REP1.sorted.bam.idxstats",
+            "RAP1_UNINDUCED_REP1.sorted.bam.stats",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats",
+            "RAP1_UNINDUCED_REP2.sorted.bam.flagstat",
+            "RAP1_UNINDUCED_REP2.sorted.bam.idxstats",
+            "RAP1_UNINDUCED_REP2.sorted.bam.stats",
+            "WT_REP1.sorted.bam.flagstat",
+            "WT_REP1.sorted.bam.idxstats",
+            "WT_REP1.sorted.bam.stats",
+            "WT_REP2.sorted.bam.flagstat",
+            "WT_REP2.sorted.bam.idxstats",
+            "WT_REP2.sorted.bam.stats"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T19:09:21.84327"
+    },
+    "multiqc_plots": {
+        "content": [
+            "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
+            "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
+            "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
+            "dupradar-section-plot.png:md5,eacbc664cc29a7a59a6aa366b4618582",
+            "fail_mapped_samples_table.png:md5,e0702273ab75b55895e566cb2945d893",
+            "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890",
+            "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84",
+            "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f",
+            "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14",
+            "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
+            "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959",
+            "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16",
+            "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881",
+            "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e",
+            "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb",
+            "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
+            "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
+            "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2",
+            "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054",
+            "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
+            "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
+            "featurecounts_biotype_plot-cnt.png:md5,95b10627fff1af0a209b8e380f4a4d0b",
+            "featurecounts_biotype_plot-pct.png:md5,f9c1cf03824ff9ba7da8537ecd93945b",
+            "qualimap_gene_coverage_profile_Counts.png:md5,2d54a60bef3dfa978da48c1b6872c41c",
+            "qualimap_gene_coverage_profile_Normalised.png:md5,a85a901be4c08c9dfcfd9fc87d890c1e",
+            "rseqc_infer_experiment_plot.png:md5,5ce01a7b923f4e6433b76dd88ca22f42",
+            "rseqc_read_dups_plot.png:md5,bdc7281c52b54a5784aa0d714f9c255e",
+            "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f",
+            "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6",
+            "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f",
+            "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d",
+            "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d",
+            "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f",
+            "multiqc_report.html",
+            "cutadapt_filtered_reads_plot-cnt.pdf",
+            "cutadapt_filtered_reads_plot-pct.pdf",
+            "cutadapt_trimmed_sequences_plot_3_Counts.pdf",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
+            "dupradar-section-plot.pdf",
+            "fail_mapped_samples_table.pdf",
+            "fail_strand_check_table.pdf",
+            "fastqc-status-check-heatmap-1.pdf",
+            "fastqc-status-check-heatmap.pdf",
+            "fastqc_adapter_content_plot.pdf",
+            "fastqc_overrepresented_sequences_plot-1.pdf",
+            "fastqc_overrepresented_sequences_plot.pdf",
+            "fastqc_per_base_n_content_plot-1.pdf",
+            "fastqc_per_base_n_content_plot.pdf",
+            "fastqc_per_base_sequence_quality_plot-1.pdf",
+            "fastqc_per_base_sequence_quality_plot.pdf",
+            "fastqc_per_sequence_gc_content_plot-1_Counts.pdf",
+            "fastqc_per_sequence_gc_content_plot-1_Percentages.pdf",
+            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
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+            "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
+            "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+            "multiqc_featurecounts_biotype_plot.txt:md5,f3c566d2eaf6bf2ffe5ad12036ce3500",
+            "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
+            "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+            "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+            "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+            "qualimap_gene_coverage_profile_Counts.txt:md5,6d377444d29c3d4135980982ab1df2fb",
+            "qualimap_gene_coverage_profile_Normalised.txt:md5,dc8b4f9fddc08e06668f9ee87faac008",
+            "qualimap_rnaseq_cov_hist.txt:md5,a409821701f60811027daef4e7f3ebee",
+            "rseqc_infer_experiment_plot.txt:md5,749a802379ada3ec9d2083ecbe6aef7e",
+            "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
+            "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
+            "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
+            "fastqc_top_overrepresented_sequences_table-1.txt",
+            "fastqc_top_overrepresented_sequences_table.txt",
+            "junction_saturation_known.txt",
+            "junction_saturation_novel.txt",
+            "multiqc_data.json",
+            "multiqc_dupradar-section-plot.txt",
+            "multiqc_fail_strand_check_table.txt",
+            "multiqc_general_stats.txt",
+            "multiqc_picard_dups.txt",
+            "multiqc_rseqc_bam_stat.txt",
+            "multiqc_rseqc_infer_experiment.txt",
+            "multiqc_rseqc_junction_annotation.txt",
+            "multiqc_rseqc_read_distribution.txt",
+            "multiqc_salmon.txt",
+            "multiqc_salmon_deseq2_clustering-plot.txt",
+            "multiqc_salmon_deseq2_clustering-plot_1.txt",
+            "multiqc_salmon_deseq2_clustering-plot_2.txt",
+            "multiqc_salmon_deseq2_clustering-plot_3.txt",
+            "multiqc_salmon_deseq2_clustering-plot_4.txt",
+            "multiqc_salmon_deseq2_pca-plot.txt",
+            "multiqc_samtools_flagstat.txt",
+            "multiqc_samtools_stats.txt",
+            "multiqc_software_versions.txt",
+            "multiqc_sources.txt",
+            "multiqc_star.txt",
+            "multiqc_star_salmon_deseq2_clustering-plot.txt",
+            "multiqc_star_salmon_deseq2_clustering-plot_1.txt",
+            "multiqc_star_salmon_deseq2_clustering-plot_2.txt",
+            "multiqc_star_salmon_deseq2_clustering-plot_3.txt",
+            "multiqc_star_salmon_deseq2_clustering-plot_4.txt",
+            "multiqc_star_salmon_deseq2_pca-plot.txt",
+            "picard_deduplication.txt",
+            "qualimap_genomic_origin.txt",
+            "qualimap_rnaseq_genome_results.txt",
+            "rseqc_bam_stat.txt",
+            "rseqc_inner_distance.txt",
+            "rseqc_inner_distance_plot_Counts.txt",
+            "rseqc_inner_distance_plot_Percentages.txt",
+            "rseqc_junction_annotation_junctions_plot_Events.txt",
+            "rseqc_junction_annotation_junctions_plot_Junctions.txt",
+            "rseqc_junction_saturation_all.txt",
+            "rseqc_junction_saturation_plot_All_Junctions.txt",
+            "rseqc_junction_saturation_plot_Known_Junctions.txt",
+            "rseqc_junction_saturation_plot_Novel_Junctions.txt",
+            "rseqc_read_distribution_plot.txt",
+            "rseqc_read_dups.txt",
+            "rseqc_read_dups_plot.txt",
+            "salmon_plot.txt",
+            "samtools-flagstat-dp_Percentage_of_total.txt",
+            "samtools-flagstat-dp_Read_counts.txt",
+            "samtools-stats-dp.txt",
+            "samtools_alignment_plot.txt",
+            "star_alignment_plot.txt",
+            "star_summary_table.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T19:09:21.700284"
+    },
+    "star_salmon/deseq2_qc": {
+        "content": [
+            "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
+            "RAP1_IAA_30M_REP1.txt",
+            "RAP1_UNINDUCED_REP1.txt",
+            "RAP1_UNINDUCED_REP2.txt",
+            "WT_REP1.txt",
+            "WT_REP2.txt",
+            "deseq2.size_factors.RData",
+            "deseq2.dds.RData",
+            "deseq2.pca.vals.txt",
+            "deseq2.plots.pdf",
+            "deseq2.sample.dists.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:20:15.658024"
+    },
+    "star_salmon/markdup": {
+        "content": [
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam",
+            "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:36:12.596967"
+    },
+    "star_salmon/featurecounts": {
+        "content": [
+            "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b",
+            "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
+            "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212",
+            "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9",
+            "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb",
+            "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5",
+            "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4",
+            "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0",
+            "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8",
+            "RAP1_IAA_30M_REP1.featureCounts.txt.summary",
+            "RAP1_UNINDUCED_REP1.featureCounts.txt.summary",
+            "RAP1_UNINDUCED_REP2.featureCounts.txt.summary"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:06:36.957812"
+    },
+    "salmon/deseq2_qc": {
+        "content": [
+            "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
+            "deseq2.dds.RData",
+            "deseq2.pca.vals.txt",
+            "deseq2.plots.pdf",
+            "deseq2.sample.dists.txt",
+            "RAP1_IAA_30M_REP1.txt",
+            "RAP1_UNINDUCED_REP1.txt",
+            "RAP1_UNINDUCED_REP2.txt",
+            "WT_REP1.txt",
+            "WT_REP2.txt",
+            "deseq2.size_factors.RData"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:04:54.964861"
+    },
+    "salmon": {
+        "content": [
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "salmon.merged.gene_counts.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts.tsv",
+            "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_length_scaled.tsv",
+            "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_scaled.tsv",
+            "salmon.merged.gene_lengths.tsv",
+            "salmon.merged.gene_tpm.tsv",
+            "salmon.merged.transcript_counts.SummarizedExperiment.rds",
+            "salmon.merged.transcript_counts.tsv",
+            "salmon.merged.transcript_lengths.tsv",
+            "salmon.merged.transcript_tpm.tsv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:04:55.21324"
+    },
+    "star_salmon/picard_metrics": {
+        "content": [
+            "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:36:12.280587"
+    },
+    "star_salmon/salmon": {
+        "content": [
+            "salmon.merged.gene_counts.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts.tsv",
+            "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_length_scaled.tsv",
+            "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_scaled.tsv",
+            "salmon.merged.gene_lengths.tsv",
+            "salmon.merged.gene_tpm.tsv",
+            "salmon.merged.transcript_counts.SummarizedExperiment.rds",
+            "salmon.merged.transcript_counts.tsv",
+            "salmon.merged.transcript_lengths.tsv",
+            "salmon.merged.transcript_tpm.tsv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:36:12.406892"
+    },
+    "star_salmon/bigwig": {
+        "content": [
+            "RAP1_IAA_30M_REP1.forward.bigWig",
+            "RAP1_IAA_30M_REP1.reverse.bigWig",
+            "RAP1_UNINDUCED_REP1.forward.bigWig",
+            "RAP1_UNINDUCED_REP1.reverse.bigWig",
+            "RAP1_UNINDUCED_REP2.forward.bigWig",
+            "RAP1_UNINDUCED_REP2.reverse.bigWig"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:20:15.635275"
+    },
+    "versions": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:36:12.954252"
+    },
+    "fastqc/trim": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip",
+            "WT_REP1_trimmed_1_val_1_fastqc.html",
+            "WT_REP1_trimmed_1_val_1_fastqc.zip",
+            "WT_REP1_trimmed_2_val_2_fastqc.html",
+            "WT_REP1_trimmed_2_val_2_fastqc.zip",
+            "WT_REP2_trimmed_1_val_1_fastqc.html",
+            "WT_REP2_trimmed_1_val_1_fastqc.zip",
+            "WT_REP2_trimmed_2_val_2_fastqc.html",
+            "WT_REP2_trimmed_2_val_2_fastqc.zip"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:04:54.759052"
+    },
+    "star_salmon/dupradar": {
+        "content": [
+            "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217",
+            "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370",
+            "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b",
+            "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
+            "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
+            "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
+            "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf",
+            "RAP1_IAA_30M_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP2_expressionHist.pdf",
+            "RAP1_IAA_30M_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpDens.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:36:12.202189"
+    },
+    "bbsplit": {
+        "content": [
+            "RAP1_IAA_30M_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP2.stats.txt",
+            "WT_REP1.stats.txt",
+            "WT_REP2.stats.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T16:04:54.719906"
+    },
+    "star_salmon/qualimap": {
+        "content": [
+            "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d",
+            "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4",
+            "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a",
+            "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37",
+            "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8",
+            "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
+            "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
+            "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518",
+            "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d",
+            "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50",
+            "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe",
+            "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3",
+            "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff",
+            "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff",
+            "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58",
+            "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90",
+            "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8",
+            "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518",
+            "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e",
+            "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d",
+            "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:06:37.041504"
+    }
+}
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 000000000..6bf8f2929
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,41 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
+
+params {
+    // Base directory for nf-core/modules test data
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
+
+    // Base directory for nf-core/rnaseq test data
+    pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/'
+
+    // for hisat2
+    hisat2_build_memory = '3.GB'
+
+    validationSchemaIgnoreParams = 'genomes,igenomes_base,modules_testdata_base_path,pipelines_testdata_base_path'
+
+    // TODO: check if we rather do this or disable publishdir for all processes when testing modules/subworkflows
+    outdir = 'results'
+}
+
+// Impose sensible resource limits for testing
+process {
+    withName: '.*' {
+        cpus   = 2
+        memory = 3.GB
+        time   = 2.h
+    }
+}
+
+// Impose same minimum Nextflow version as the pipeline for testing
+manifest {
+    nextflowVersion = '!>=23.04.0'
+}
+
+// Disable all Nextflow reporting options
+timeline { enabled = false }
+report   { enabled = false }
+trace    { enabled = false }
+dag      { enabled = false }
diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test
new file mode 100644
index 000000000..430f18b6f
--- /dev/null
+++ b/tests/remove_ribo_rna.nf.test
@@ -0,0 +1,978 @@
+nextflow_pipeline {
+
+    name "Test pipeline with ribosomal RNA removal"
+    script "../main.nf"
+
+    test("Params: --remove_ribo_rna") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                remove_ribo_rna = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name
+                ).match("fastqc/raw") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name
+                ).match("fastqc/trim") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/sortmerna-detailed-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-pct.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
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+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name
+                ).match("salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.sf").name
+                ).match("salmon_quant") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/sortmerna/RAP1_IAA_30M_REP1.sortmerna.log").name,
+                    file("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP1.sortmerna.log").name,
+                    file("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP2.sortmerna.log").name,
+                    file("${params.outdir}/sortmerna/WT_REP1.sortmerna.log").name,
+                    file("${params.outdir}/sortmerna/WT_REP2.sortmerna.log").name
+                ).match("star_salmon/sortmerna") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name
+                ).match("star_salmon/bigwig") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name
+                ).match("star_salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"),
+                    // PDFs are not stable
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name
+                ).match("star_salmon/dupradar") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"),
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary").name
+                ).match("star_salmon/featurecounts") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"),
+                    // Logs are not stable
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name
+                ).match("star_salmon/log") },
+                { assert snapshot(
+                    // Metrics are not stable
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name
+                ).match("star_salmon/picard_metrics") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    // HTML reports and these files are not stable
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name
+                ).match("star_salmon/qualimap") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"),
+                    // PDFs, R scripts and all these files are not stable
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name
+                ).match("star_salmon/rseqc") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("star_salmon/salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name
+                ).match("star_salmon/samtools_stats") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name
+                ).match("star_salmon/stringtie") },
+                { assert snapshot(
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name
+                ).match("star_salmon/markdup") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name
+                ).match("star_salmon/salmon_quant") },
+                { assert snapshot(
+                    // These reports are not stable
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match("trimgalore") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    test("Params: --remove_ribo_rna - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                remove_ribo_rna = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    file("${params.outdir}/custom/out/genome_transcriptome.fasta").name,
+                    file("${params.outdir}/custom/out/genome_transcriptome.gtf").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
new file mode 100644
index 000000000..73cd09c7c
--- /dev/null
+++ b/tests/remove_ribo_rna.nf.test.snap
@@ -0,0 +1,1102 @@
+{
+    "star_salmon/log": {
+        "content": [
+            "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee",
+            "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8",
+            "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
+            "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204",
+            "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23",
+            "RAP1_IAA_30M_REP1.Log.final.out",
+            "RAP1_IAA_30M_REP1.Log.out",
+            "RAP1_IAA_30M_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP1.Log.final.out",
+            "RAP1_UNINDUCED_REP1.Log.out",
+            "RAP1_UNINDUCED_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP2.Log.final.out",
+            "RAP1_UNINDUCED_REP2.Log.out",
+            "RAP1_UNINDUCED_REP2.Log.progress.out",
+            "WT_REP1.Log.final.out",
+            "WT_REP1.Log.out",
+            "WT_REP1.Log.progress.out",
+            "WT_REP2.Log.final.out",
+            "WT_REP2.Log.out",
+            "WT_REP2.Log.progress.out"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:12.426991"
+    },
+    "star_salmon/salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,6cd02367152bb2dd59a6f1f70df2d7f8",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020",
+            "ambig_info.tsv:md5,8611b6c03f6aa1a5f3dfceb0e65ad4ef",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5",
+            "ambig_info.tsv:md5,1b69f9b651dfa6799e310004c1e3309f",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748",
+            "ambig_info.tsv:md5,070c7d50eab5ce0f211cdb06f9d7cc29",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde",
+            "ambig_info.tsv:md5,b8c61854b56a1c9a0fc8f158ea0c7599",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae",
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:13.580621"
+    },
+    "trimgalore": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:13.706881"
+    },
+    "star_salmon/rseqc": {
+        "content": [
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+        "content": [
+            "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f36792d25b268b6d556f8728300f4afc",
+            "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
+            "RAP1_IAA_30M_REP1.featureCounts.txt:md5,c5865ded7168476d93057d2aedaec694",
+            "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,782f5001d411ba79314ba77f7d36b157",
+            "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb",
+            "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a0fb30c2b937a5a41ac865ab09367af7",
+            "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,1c9d07d9f9d12219d2b9f761f854eced",
+            "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0",
+            "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,de016e691f5d56b13bbaa626ce2cc93e",
+            "WT_REP1.biotype_counts_mqc.tsv:md5,eca4a76b9243248d01df5f4289b8201e",
+            "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9",
+            "WT_REP1.featureCounts.txt:md5,7aadafd0a26f5047a9ae7266eccfce05",
+            "WT_REP2.biotype_counts_mqc.tsv:md5,530605b80da27915a90d452249f3243a",
+            "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481",
+            "WT_REP2.featureCounts.txt:md5,809af01851125c401d576c21efca7b5a",
+            "RAP1_IAA_30M_REP1.featureCounts.txt.summary",
+            "RAP1_UNINDUCED_REP1.featureCounts.txt.summary",
+            "RAP1_UNINDUCED_REP2.featureCounts.txt.summary",
+            "WT_REP1.featureCounts.txt.summary",
+            "WT_REP2.featureCounts.txt.summary"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:19:35.982363"
+    },
+    "salmon/deseq2_qc": {
+        "content": [
+            "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
+            "deseq2.dds.RData",
+            "deseq2.pca.vals.txt",
+            "deseq2.plots.pdf",
+            "deseq2.sample.dists.txt",
+            "RAP1_IAA_30M_REP1.txt",
+            "RAP1_UNINDUCED_REP1.txt",
+            "RAP1_UNINDUCED_REP2.txt",
+            "WT_REP1.txt",
+            "WT_REP2.txt",
+            "deseq2.size_factors.RData"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:11.010569"
+    },
+    "salmon": {
+        "content": [
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "salmon.merged.gene_counts.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts.tsv",
+            "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_length_scaled.tsv",
+            "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_scaled.tsv",
+            "salmon.merged.gene_lengths.tsv",
+            "salmon.merged.gene_tpm.tsv",
+            "salmon.merged.transcript_counts.SummarizedExperiment.rds",
+            "salmon.merged.transcript_counts.tsv",
+            "salmon.merged.transcript_lengths.tsv",
+            "salmon.merged.transcript_tpm.tsv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:11.336679"
+    },
+    "star_salmon/picard_metrics": {
+        "content": [
+            "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt",
+            "WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt",
+            "WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:12.629115"
+    },
+    "star_salmon/salmon": {
+        "content": [
+            "salmon.merged.gene_counts.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts.tsv",
+            "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_length_scaled.tsv",
+            "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_scaled.tsv",
+            "salmon.merged.gene_lengths.tsv",
+            "salmon.merged.gene_tpm.tsv",
+            "salmon.merged.transcript_counts.SummarizedExperiment.rds",
+            "salmon.merged.transcript_counts.tsv",
+            "salmon.merged.transcript_lengths.tsv",
+            "salmon.merged.transcript_tpm.tsv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:13.112566"
+    },
+    "star_salmon/bigwig": {
+        "content": [
+            "RAP1_IAA_30M_REP1.forward.bigWig",
+            "RAP1_IAA_30M_REP1.reverse.bigWig",
+            "RAP1_UNINDUCED_REP1.forward.bigWig",
+            "RAP1_UNINDUCED_REP1.reverse.bigWig",
+            "RAP1_UNINDUCED_REP2.forward.bigWig",
+            "RAP1_UNINDUCED_REP2.reverse.bigWig",
+            "WT_REP1.forward.bigWig",
+            "WT_REP1.reverse.bigWig",
+            "WT_REP2.forward.bigWig",
+            "WT_REP2.reverse.bigWig"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:18:52.080654"
+    },
+    "star_salmon/sortmerna": {
+        "content": [
+            "RAP1_IAA_30M_REP1.sortmerna.log",
+            "RAP1_UNINDUCED_REP1.sortmerna.log",
+            "RAP1_UNINDUCED_REP2.sortmerna.log",
+            "WT_REP1.sortmerna.log",
+            "WT_REP2.sortmerna.log"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:18:51.881667"
+    },
+    "versions": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:14.01652"
+    },
+    "fastqc/trim": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip",
+            "WT_REP1_trimmed_1_val_1_fastqc.html",
+            "WT_REP1_trimmed_1_val_1_fastqc.zip",
+            "WT_REP1_trimmed_2_val_2_fastqc.html",
+            "WT_REP1_trimmed_2_val_2_fastqc.zip",
+            "WT_REP2_trimmed_1_val_1_fastqc.html",
+            "WT_REP2_trimmed_1_val_1_fastqc.zip",
+            "WT_REP2_trimmed_2_val_2_fastqc.html",
+            "WT_REP2_trimmed_2_val_2_fastqc.zip"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:10.790876"
+    },
+    "star_salmon/dupradar": {
+        "content": [
+            "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,ddadea4a08511aae6faeb632eb6aafea",
+            "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1db4c86723cf69052c4386760a9750bb",
+            "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc",
+            "WT_REP1_dupMatrix.txt:md5,b0de1683f2a9bfa42437e924a11648fd",
+            "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677",
+            "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,b21a53b0156b0afdfc28c237cb11218d",
+            "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,eccc5ca37855c717d35477e684188695",
+            "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217",
+            "WT_REP1_intercept_slope.txt:md5,f38c8525b7fcb990b7158f1518e451ad",
+            "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2",
+            "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf",
+            "WT_REP1_duprateExpBoxplot.pdf",
+            "WT_REP2_duprateExpBoxplot.pdf",
+            "RAP1_IAA_30M_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP2_expressionHist.pdf",
+            "WT_REP1_expressionHist.pdf",
+            "WT_REP2_expressionHist.pdf",
+            "RAP1_IAA_30M_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpDens.pdf",
+            "WT_REP1_duprateExpDens.pdf",
+            "WT_REP2_duprateExpDens.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:12.064305"
+    },
+    "bbsplit": {
+        "content": [
+            "RAP1_IAA_30M_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP2.stats.txt",
+            "WT_REP1.stats.txt",
+            "WT_REP2.stats.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T18:00:10.74095"
+    },
+    "star_salmon/qualimap": {
+        "content": [
+            "Coverage Profile Along Genes (High).png:md5,1a837e43161d7133e9156c7b18123aa9",
+            "Coverage Profile Along Genes (Low).png:md5,46c5ba09af49602b956efd780f7a39e4",
+            "Coverage Profile Along Genes (Total).png:md5,b04cac9c2d15b1b9623d87d44caadff6",
+            "Transcript coverage histogram.png:md5,cbb250c6903bfe6ecab5fb4b2ca661e5",
+            "coverage_profile_along_genes_(high).txt:md5,5aee6c959137a8c9bfbd0ddaa79dddba",
+            "coverage_profile_along_genes_(low).txt:md5,d2742410803e0de7cc606ef118010ea8",
+            "coverage_profile_along_genes_(total).txt:md5,d2742410803e0de7cc606ef118010ea8",
+            "Coverage Profile Along Genes (High).png:md5,8c8b46f9bfb6cf952a95d85a6b917444",
+            "Coverage Profile Along Genes (Low).png:md5,5c56671f085c6db7fd86b41bb5b7e6d0",
+            "Coverage Profile Along Genes (Total).png:md5,b83fbaedfe4dcfdd7b3970d2ff27d517",
+            "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe",
+            "coverage_profile_along_genes_(high).txt:md5,f5ac8f74fcad5d9ac72dbb6b65184bd0",
+            "coverage_profile_along_genes_(low).txt:md5,d66da6e3f49b0870184fc881a162e785",
+            "coverage_profile_along_genes_(total).txt:md5,d66da6e3f49b0870184fc881a162e785",
+            "Coverage Profile Along Genes (High).png:md5,015aa34b0d32f38bade831a3ef497984",
+            "Coverage Profile Along Genes (Low).png:md5,5798e0d977e0fee55ec4fc5192bfc0f4",
+            "Coverage Profile Along Genes (Total).png:md5,2bbec5e165075024cb1f74a042b1385a",
+            "Transcript coverage histogram.png:md5,bfd09f8b3282958a6a73b7924edac664",
+            "coverage_profile_along_genes_(high).txt:md5,634f447f91db940d2148af74cf36febd",
+            "coverage_profile_along_genes_(low).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3",
+            "coverage_profile_along_genes_(total).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3",
+            "Coverage Profile Along Genes (High).png:md5,d8a36870a6f262c41995b4b5bd26a149",
+            "Coverage Profile Along Genes (Low).png:md5,5570af90ee685a3c95117519aa6bdc46",
+            "Coverage Profile Along Genes (Total).png:md5,eb53e699213ce453cbea7f71f5204b08",
+            "Transcript coverage histogram.png:md5,f0bd8d82a8b7adec6e1f1ef85633eded",
+            "coverage_profile_along_genes_(high).txt:md5,a349232d75f6c0adab6afcd9f6cbbafb",
+            "coverage_profile_along_genes_(low).txt:md5,b2c696661e6c524b1641eb7267c70edc",
+            "coverage_profile_along_genes_(total).txt:md5,b2c696661e6c524b1641eb7267c70edc",
+            "Coverage Profile Along Genes (High).png:md5,3c1c603d63f3f7f9ba1ab6e7749b7771",
+            "Coverage Profile Along Genes (Low).png:md5,9f80251ed043cf900fa939cc254ccc81",
+            "Coverage Profile Along Genes (Total).png:md5,a420f287f986a8db317be712ac0a2237",
+            "Transcript coverage histogram.png:md5,c467c5eac12a95f8569198927434440d",
+            "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294",
+            "coverage_profile_along_genes_(low).txt:md5,b9be191fdec82c78057e083d3adf20dd",
+            "coverage_profile_along_genes_(total).txt:md5,b9be191fdec82c78057e083d3adf20dd",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:19:36.107982"
+    }
+}
\ No newline at end of file
diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test
new file mode 100644
index 000000000..9105ed9fa
--- /dev/null
+++ b/tests/salmon.nf.test
@@ -0,0 +1,275 @@
+nextflow_pipeline {
+
+    name "Test pipeline with Salmon, skipping both QC and alignment"
+    script "../main.nf"
+
+    test("Params: --pseudo_aligner salmon --skip_qc --skip_alignment") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                pseudo_aligner = 'salmon'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name
+                ).match("fastqc/trim") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/multiqc_cutadapt.txt"),
+                    path("${params.outdir}/multiqc/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_salmon.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/multiqc_sources.txt").name,
+                    file("${params.outdir}/multiqc/multiqc_report_data/salmon_plot.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/general_stats_table.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/pdf/salmon_plot.pdf").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/general_stats_table.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/png/salmon_plot.png").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/general_stats_table.svg").name,
+                    file("${params.outdir}/multiqc/multiqc_report_plots/svg/salmon_plot.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.sf").name
+                ).match("salmon_quant") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("salmon") },
+                { assert snapshot(
+                    // These reports are not stable
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match("trimgalore") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    test("Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                pseudo_aligner = 'salmon'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    file("${params.outdir}/custom/out/genome_transcriptome.fasta").name,
+                    file("${params.outdir}/custom/out/genome_transcriptome.gtf").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name,
+                    file("${params.outdir}/multiqc/multiqc_report.html").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap
new file mode 100644
index 000000000..93f7cc786
--- /dev/null
+++ b/tests/salmon.nf.test.snap
@@ -0,0 +1,297 @@
+{
+    "multiqc_data": {
+        "content": [
+            "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+            "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
+            "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+            "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+            "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+            "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+            "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+            "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+            "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+            "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c",
+            "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
+            "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+            "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150",
+            "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
+            "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+            "fastqc_top_overrepresented_sequences_table.txt",
+            "multiqc_data.json",
+            "multiqc_general_stats.txt",
+            "multiqc_salmon.txt",
+            "multiqc_software_versions.txt",
+            "multiqc_sources.txt",
+            "salmon_plot.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:09.703525"
+    },
+    "trimgalore": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:09.861436"
+    },
+    "references": {
+        "content": [
+            "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
+            "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:09.678308"
+    },
+    "versions": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:10.110511"
+    },
+    "fastqc/trim": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip",
+            "WT_REP1_trimmed_1_val_1_fastqc.html",
+            "WT_REP1_trimmed_1_val_1_fastqc.zip",
+            "WT_REP1_trimmed_2_val_2_fastqc.html",
+            "WT_REP1_trimmed_2_val_2_fastqc.zip",
+            "WT_REP2_trimmed_1_val_1_fastqc.html",
+            "WT_REP2_trimmed_1_val_1_fastqc.zip",
+            "WT_REP2_trimmed_2_val_2_fastqc.html",
+            "WT_REP2_trimmed_2_val_2_fastqc.zip"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:09.69038"
+    },
+    "salmon": {
+        "content": [
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "salmon.merged.gene_counts.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts.tsv",
+            "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_length_scaled.tsv",
+            "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_scaled.tsv",
+            "salmon.merged.gene_lengths.tsv",
+            "salmon.merged.gene_tpm.tsv",
+            "salmon.merged.transcript_counts.SummarizedExperiment.rds",
+            "salmon.merged.transcript_counts.tsv",
+            "salmon.merged.transcript_lengths.tsv",
+            "salmon.merged.transcript_tpm.tsv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:09.804203"
+    },
+    "multiqc_plots": {
+        "content": [
+            "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
+            "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
+            "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
+            "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890",
+            "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f",
+            "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
+            "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959",
+            "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e",
+            "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
+            "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
+            "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
+            "multiqc_report.html",
+            "cutadapt_filtered_reads_plot-cnt.pdf",
+            "cutadapt_filtered_reads_plot-pct.pdf",
+            "cutadapt_trimmed_sequences_plot_3_Counts.pdf",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
+            "fastqc-status-check-heatmap.pdf",
+            "fastqc_overrepresented_sequences_plot.pdf",
+            "fastqc_per_base_n_content_plot.pdf",
+            "fastqc_per_base_sequence_quality_plot.pdf",
+            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+            "fastqc_per_sequence_quality_scores_plot.pdf",
+            "fastqc_sequence_counts_plot-cnt.pdf",
+            "fastqc_sequence_counts_plot-pct.pdf",
+            "fastqc_sequence_duplication_levels_plot.pdf",
+            "fastqc_sequence_length_distribution_plot.pdf",
+            "fastqc_top_overrepresented_sequences_table.pdf",
+            "general_stats_table.pdf",
+            "salmon_plot.pdf",
+            "fastqc_per_base_n_content_plot.png",
+            "fastqc_per_base_sequence_quality_plot.png",
+            "fastqc_sequence_length_distribution_plot.png",
+            "fastqc_top_overrepresented_sequences_table.png",
+            "general_stats_table.png",
+            "salmon_plot.png",
+            "cutadapt_filtered_reads_plot-cnt.svg",
+            "cutadapt_filtered_reads_plot-pct.svg",
+            "cutadapt_trimmed_sequences_plot_3_Counts.svg",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
+            "fastqc-status-check-heatmap.svg",
+            "fastqc_overrepresented_sequences_plot.svg",
+            "fastqc_per_base_n_content_plot.svg",
+            "fastqc_per_base_sequence_quality_plot.svg",
+            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+            "fastqc_per_sequence_quality_scores_plot.svg",
+            "fastqc_sequence_counts_plot-cnt.svg",
+            "fastqc_sequence_counts_plot-pct.svg",
+            "fastqc_sequence_duplication_levels_plot.svg",
+            "fastqc_sequence_length_distribution_plot.svg",
+            "fastqc_top_overrepresented_sequences_table.svg",
+            "general_stats_table.svg",
+            "salmon_plot.svg"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:09.724424"
+    },
+    "bbsplit": {
+        "content": [
+            "RAP1_IAA_30M_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP2.stats.txt",
+            "WT_REP1.stats.txt",
+            "WT_REP2.stats.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:09.665867"
+    },
+    "salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c",
+            "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1",
+            "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636",
+            "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935",
+            "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326",
+            "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3",
+            "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d",
+            "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6",
+            "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac",
+            "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:09.758031"
+    },
+    "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}",
+            "genome_transcriptome.fasta",
+            "genome_transcriptome.gtf",
+            "RAP1_IAA_30M_REP1_raw.html",
+            "RAP1_IAA_30M_REP1_raw.zip",
+            "RAP1_UNINDUCED_REP1_raw.html",
+            "RAP1_UNINDUCED_REP1_raw.zip",
+            "RAP1_UNINDUCED_REP2_raw.html",
+            "RAP1_UNINDUCED_REP2_raw.zip",
+            "WT_REP1_raw.html",
+            "WT_REP1_raw.zip",
+            "WT_REP2_raw.html",
+            "WT_REP2_raw.zip",
+            "multiqc_report.html",
+            "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt",
+            "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt",
+            "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:25:58.654392"
+    }
+}
\ No newline at end of file
diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test
new file mode 100644
index 000000000..8fd703462
--- /dev/null
+++ b/tests/skip_qc.nf.test
@@ -0,0 +1,527 @@
+nextflow_pipeline {
+
+    name "Test pipeline by skipping QC options"
+    script "../main.nf"
+
+    test("Params: --skip_qc") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                skip_qc = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name
+                ).match("fastqc/trim") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name
+                ).match("star_salmon/samtools_stats") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name
+                ).match("star_salmon/stringtie") },
+                { assert snapshot(
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name
+                ).match("star_salmon/markdup") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.sf").name
+                ).match("salmon_quant") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name
+                ).match("star_salmon/bigwig") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"),
+                    // Logs are not stable
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name
+                ).match("star_salmon/log") },
+                { assert snapshot(
+                    // Metrics are not stable
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name
+                ).match("star_salmon/picard_metrics") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name
+                ).match("star_salmon/salmon_quant") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("star_salmon/salmon") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    test("Params: --skip_qc - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                skip_qc = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    file("${params.outdir}/custom/out/genome_transcriptome.fasta").name,
+                    file("${params.outdir}/custom/out/genome_transcriptome.gtf").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap
new file mode 100644
index 000000000..563f4913e
--- /dev/null
+++ b/tests/skip_qc.nf.test.snap
@@ -0,0 +1,596 @@
+{
+    "star_salmon/log": {
+        "content": [
+            "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee",
+            "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8",
+            "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
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+    "star_salmon/picard_metrics": {
+        "content": [
+            "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt",
+            "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt",
+            "RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt",
+            "WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt",
+            "WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:11:58.412083"
+    },
+    "star_salmon/salmon": {
+        "content": [
+            "salmon.merged.gene_counts.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts.tsv",
+            "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_length_scaled.tsv",
+            "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds",
+            "salmon.merged.gene_counts_scaled.tsv",
+            "salmon.merged.gene_lengths.tsv",
+            "salmon.merged.gene_tpm.tsv",
+            "salmon.merged.transcript_counts.SummarizedExperiment.rds",
+            "salmon.merged.transcript_counts.tsv",
+            "salmon.merged.transcript_lengths.tsv",
+            "salmon.merged.transcript_tpm.tsv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:11:58.679186"
+    },
+    "star_salmon/bigwig": {
+        "content": [
+            "RAP1_IAA_30M_REP1.forward.bigWig",
+            "RAP1_IAA_30M_REP1.reverse.bigWig",
+            "RAP1_UNINDUCED_REP1.forward.bigWig",
+            "RAP1_UNINDUCED_REP1.reverse.bigWig",
+            "RAP1_UNINDUCED_REP2.forward.bigWig",
+            "RAP1_UNINDUCED_REP2.reverse.bigWig",
+            "WT_REP1.forward.bigWig",
+            "WT_REP1.reverse.bigWig",
+            "WT_REP2.forward.bigWig",
+            "WT_REP2.reverse.bigWig"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:11:58.232941"
+    },
+    "star_salmon/stringtie": {
+        "content": [
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,3f149502efe2a9d4bac98b1dd18c15e7",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,a052ab04070e72cc318fb7680b0764e3",
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,e82329a443b9ff50a86e42aff91bd704",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a",
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,10e2d00f93f9e74f224bd3c1bfbeb29b",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e",
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8",
+            "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
+            "e_data.ctab:md5,b03f3118d1aa58fceadcb3311028e856",
+            "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
+            "i_data.ctab:md5,041edee3193df311f621c09f4991892b",
+            "t_data.ctab",
+            "RAP1_IAA_30M_REP1.coverage.gtf",
+            "RAP1_IAA_30M_REP1.gene.abundance.txt",
+            "RAP1_IAA_30M_REP1.transcripts.gtf",
+            "t_data.ctab",
+            "RAP1_UNINDUCED_REP1.coverage.gtf",
+            "RAP1_UNINDUCED_REP1.gene.abundance.txt",
+            "RAP1_UNINDUCED_REP1.transcripts.gtf",
+            "t_data.ctab",
+            "RAP1_UNINDUCED_REP2.coverage.gtf",
+            "RAP1_UNINDUCED_REP2.gene.abundance.txt",
+            "RAP1_UNINDUCED_REP2.transcripts.gtf",
+            "t_data.ctab",
+            "WT_REP1.coverage.gtf",
+            "WT_REP1.gene.abundance.txt",
+            "WT_REP1.transcripts.gtf",
+            "t_data.ctab",
+            "WT_REP2.coverage.gtf",
+            "WT_REP2.gene.abundance.txt",
+            "WT_REP2.transcripts.gtf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:11:57.943545"
+    },
+    "versions": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:11:59.164489"
+    },
+    "fastqc/trim": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip",
+            "WT_REP1_trimmed_1_val_1_fastqc.html",
+            "WT_REP1_trimmed_1_val_1_fastqc.zip",
+            "WT_REP1_trimmed_2_val_2_fastqc.html",
+            "WT_REP1_trimmed_2_val_2_fastqc.zip",
+            "WT_REP2_trimmed_1_val_1_fastqc.html",
+            "WT_REP2_trimmed_1_val_1_fastqc.zip",
+            "WT_REP2_trimmed_2_val_2_fastqc.html",
+            "WT_REP2_trimmed_2_val_2_fastqc.zip"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T11:24:48.114664"
+    },
+    "bbsplit": {
+        "content": [
+            "RAP1_IAA_30M_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP2.stats.txt",
+            "WT_REP1.stats.txt",
+            "WT_REP2.stats.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T11:24:48.0918"
+    },
+    "salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c",
+            "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1",
+            "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636",
+            "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935",
+            "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326",
+            "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3",
+            "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d",
+            "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6",
+            "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac",
+            "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:11:58.071145"
+    }
+}
\ No newline at end of file
diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test
new file mode 100644
index 000000000..e5b3aa080
--- /dev/null
+++ b/tests/skip_trimming.nf.test
@@ -0,0 +1,830 @@
+nextflow_pipeline {
+
+    name "Test pipeline by skipping trimming options"
+    script "../main.nf"
+
+    test("Params: --skip_trimming") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                skip_trimming = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name
+                ).match("fastqc/raw") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name
+                ).match("salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.sf").name
+                ).match("salmon_quant") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name
+                ).match("star_salmon/bigwig") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name
+                ).match("star_salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"),
+                    // PDFs are not stable
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name
+                ).match("star_salmon/dupradar") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"),
+                    // These files are unstable
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary").name
+                ).match("star_salmon/featurecounts") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"),
+                    path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"),
+                    // Logs are not stable
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name,
+                    file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name
+                ).match("star_salmon/log") },
+                { assert snapshot(
+                    // Metrics are not stable
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name
+                ).match("star_salmon/picard_metrics") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    // HTML reports and these files are not stable
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name
+                ).match("star_salmon/qualimap") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"),
+                    // PDFs, R scripts and all these files are not stable
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name
+                ).match("star_salmon/rseqc") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("star_salmon/salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name
+                ).match("star_salmon/samtools_stats") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name
+                ).match("star_salmon/stringtie") },
+                { assert snapshot(
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name
+                ).match("star_salmon/markdup") },
+                { assert snapshot(
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/star_salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name
+                ).match("star_salmon/salmon_quant") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    // STUB ARE CURRENTLY NOT POSSIBLE
+
+}
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
new file mode 100644
index 000000000..da3e572cc
--- /dev/null
+++ b/tests/skip_trimming.nf.test.snap
@@ -0,0 +1,943 @@
+{
+    "star_salmon/log": {
+        "content": [
+            "RAP1_IAA_30M_REP1.SJ.out.tab:md5,20c790387ef68e041bc4ffdcd032a22f",
+            "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,ba2636236fa1d26aa72f7aff73bd41f8",
+            "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1c0458f66e4af56a56f4409c120434b3",
+            "WT_REP1.SJ.out.tab:md5,299a948b1aaf329152224ba573402a51",
+            "WT_REP2.SJ.out.tab:md5,073498a8fb5fb4da664c9129a6777c42",
+            "RAP1_IAA_30M_REP1.Log.final.out",
+            "RAP1_IAA_30M_REP1.Log.out",
+            "RAP1_IAA_30M_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP1.Log.final.out",
+            "RAP1_UNINDUCED_REP1.Log.out",
+            "RAP1_UNINDUCED_REP1.Log.progress.out",
+            "RAP1_UNINDUCED_REP2.Log.final.out",
+            "RAP1_UNINDUCED_REP2.Log.out",
+            "RAP1_UNINDUCED_REP2.Log.progress.out",
+            "WT_REP1.Log.final.out",
+            "WT_REP1.Log.out",
+            "WT_REP1.Log.progress.out",
+            "WT_REP2.Log.final.out",
+            "WT_REP2.Log.out",
+            "WT_REP2.Log.progress.out"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T15:27:29.632524"
+    },
+    "star_salmon/salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,d1d3bd2a5617220b29a9063cb29f0578",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020",
+            "ambig_info.tsv:md5,452bbc83465339d2467663b061400b95",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5",
+            "ambig_info.tsv:md5,f2aed38ba5251664024392bc89ae3f01",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748",
+            "ambig_info.tsv:md5,8d2b5ec0c441d9e078610480d179d116",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde",
+            "ambig_info.tsv:md5,44dad5d05b3c0c2ccb5a19a3a80333b3",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae",
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T15:27:31.038414"
+    },
+    "multiqc_data": {
+        "content": [
+            "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+            "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+            "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+            "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+            "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
+            "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
+            "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
+            "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
+            "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c",
+            "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
+            "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90",
+            "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
+            "multiqc_featurecounts_biotype_plot.txt:md5,567475905baa63091cfd0560fb297e10",
+            "multiqc_samtools_idxstats.txt:md5,adf5f32fa1485ad0f4dacdfedc7b4bbc",
+            "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+            "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+            "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+            "qualimap_gene_coverage_profile_Counts.txt:md5,b16bc0437cb340aaf6fa1472888b6930",
+            "qualimap_gene_coverage_profile_Normalised.txt:md5,209b0020fcd4c3c497e3abbd1f8cd593",
+            "qualimap_rnaseq_cov_hist.txt:md5,3be7bc41531ce84b42092a742bfeb0ab",
+            "rseqc_infer_experiment_plot.txt:md5,382397ae264336395e2a3b03af8d7023",
+            "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
+            "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
+            "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a557130553131c893398532377d3b525",
+            "fastqc_top_overrepresented_sequences_table.txt",
+            "junction_saturation_known.txt",
+            "junction_saturation_novel.txt",
+            "multiqc_data.json",
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+            "lib_format_counts.json:md5,4bf135c93c37f90c493f761f2709a28b",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T15:27:28.672506"
+    },
+    "star_salmon/qualimap": {
+        "content": [
+            "Coverage Profile Along Genes (High).png:md5,3a6e83a9a2e0e983b1191a622bfc8ef1",
+            "Coverage Profile Along Genes (Low).png:md5,1f075e71d4c281be2ecad16cf13f52bc",
+            "Coverage Profile Along Genes (Total).png:md5,f32d6ff38cfe4d01c6cbc917cb6e21c1",
+            "Transcript coverage histogram.png:md5,4e4a8d520a3018a888e5840936e9f4e0",
+            "coverage_profile_along_genes_(high).txt:md5,59a01cd5d9bc7b6096490d7f3d6d6877",
+            "coverage_profile_along_genes_(low).txt:md5,8a5255e6f9f142bbd22c636296f41d72",
+            "coverage_profile_along_genes_(total).txt:md5,8a5255e6f9f142bbd22c636296f41d72",
+            "Coverage Profile Along Genes (High).png:md5,a0efd6fc7c7c803a3b51e7fc4600ed98",
+            "Coverage Profile Along Genes (Low).png:md5,212d68ca87f5bc4c60ed04a33df126af",
+            "Coverage Profile Along Genes (Total).png:md5,a72b6252a3ece3fb911da724274eabae",
+            "Transcript coverage histogram.png:md5,1daabf214a2d2c32748834188c8bea5d",
+            "coverage_profile_along_genes_(high).txt:md5,61683a2fcf35174fe72a648be63d45ac",
+            "coverage_profile_along_genes_(low).txt:md5,031046ef33de379e0463fddc0b924ecd",
+            "coverage_profile_along_genes_(total).txt:md5,031046ef33de379e0463fddc0b924ecd",
+            "Coverage Profile Along Genes (High).png:md5,75dbf9d2b8bde265fdda486c050d5ff5",
+            "Coverage Profile Along Genes (Low).png:md5,8e792e6037158381a50e3668c54b7254",
+            "Coverage Profile Along Genes (Total).png:md5,beaf835a8aaf95df20815032a5f92622",
+            "Transcript coverage histogram.png:md5,6428ffa766e3c59ca42a9fb5e011d866",
+            "coverage_profile_along_genes_(high).txt:md5,2745780cc56258bbe587f9b6db03e9e4",
+            "coverage_profile_along_genes_(low).txt:md5,85154785601b18118ae2e6a19d0a1c0a",
+            "coverage_profile_along_genes_(total).txt:md5,85154785601b18118ae2e6a19d0a1c0a",
+            "Coverage Profile Along Genes (High).png:md5,6491fbf74a1444b98fdfe495b8c26a7f",
+            "Coverage Profile Along Genes (Low).png:md5,ee6b911d01b1cfbcebb5864a1f6f5fda",
+            "Coverage Profile Along Genes (Total).png:md5,f286514f978d5bcb9508a908068ff6c7",
+            "Transcript coverage histogram.png:md5,e925b300e71d23188aa45907e0754536",
+            "coverage_profile_along_genes_(high).txt:md5,6afb5ffc9ddad52f69c518e32118ac61",
+            "coverage_profile_along_genes_(low).txt:md5,248345fdf0f8de2a8d7d329edd0a5c42",
+            "coverage_profile_along_genes_(total).txt:md5,248345fdf0f8de2a8d7d329edd0a5c42",
+            "Coverage Profile Along Genes (High).png:md5,f9f0caee3156d32588c12daab8895a0f",
+            "Coverage Profile Along Genes (Low).png:md5,35ac4785ed0ffb80aaeec1fb26825f4b",
+            "Coverage Profile Along Genes (Total).png:md5,781cc1b68e9f7afc30a84b7e45b06f85",
+            "Transcript coverage histogram.png:md5,a4a300dc782deea67f18e516e0c50b3b",
+            "coverage_profile_along_genes_(high).txt:md5,f7c11dace9fc4f446fc29e5db7b3ee24",
+            "coverage_profile_along_genes_(low).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d",
+            "coverage_profile_along_genes_(total).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T15:27:29.998661"
+    }
+}
\ No newline at end of file
diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test
new file mode 100644
index 000000000..0f03bc6db
--- /dev/null
+++ b/tests/star_rsem.nf.test
@@ -0,0 +1,920 @@
+nextflow_pipeline {
+
+    name "Test pipeline with STAR aligner and RSEM for quantification"
+    script "../main.nf"
+
+    test("Params: --aligner star_rsem") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = 'star_rsem'
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name,
+                    file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name
+                ).match("bbsplit") },
+                { assert snapshot(
+                    path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                    path("${params.outdir}/custom/out/genome_gfp.gtf")
+                ).match("references") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name
+                ).match("fastqc/raw") },
+                { assert snapshot(
+                    // HTMLs and ZIPs are not stable
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name,
+                    file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name
+                ).match("fastqc/trim") },
+                { assert snapshot(
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/cutadapt_filtered_reads_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap-1.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_adapter_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_citations.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_cutadapt.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_idxstats.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram_1.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram_2.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_infer_experiment_plot.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"),
+                    // These files are not stable
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/junction_saturation_known.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/junction_saturation_novel.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_data.json").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_dupradar-section-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fail_strand_check_table.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_general_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_picard_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rsem.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_flagstat.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_stats.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_software_versions.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_sources.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_1.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_2.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_3.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_4.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_pca-plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_genomic_origin.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_assignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_multimapping_rates.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_bam_stat.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_all.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_read_distribution_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_read_dups.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_read_dups_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/salmon_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-stats-dp.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/star_alignment_plot.txt").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/star_summary_table.txt").name
+                ).match("multiqc_data") },
+                { assert snapshot(
+
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/dupradar-section-plot.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_multimapping_rates.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_dups_plot.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"),
+                    path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"),
+                    // PDFs, SVGs, some PNGs and HTML reports are not stable
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report.html").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/general_stats_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_multimapping_rates.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/salmon_plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_clustering-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_pca-plot.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_summary_table.pdf").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fail_strand_check_table.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/general_stats_table.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-pct.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_bam_stat.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/salmon_plot.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-stats-dp.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-cnt.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-pct.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_clustering-plot.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_pca-plot.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_summary_table.png").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/dupradar-section-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fail_strand_check_table.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/general_stats_table.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/picard_deduplication-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_multimapping_rates.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_bam_stat.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/salmon_plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-stats-dp.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_clustering-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_pca-plot.svg").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_summary_table.svg").name
+                ).match("multiqc_plots") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name
+                ).match("salmon/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP1/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"),
+                    path("${params.outdir}/salmon/WT_REP2/cmd_info.json"),
+                    path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP1/quant.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name,
+                    file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name,
+                    file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name,
+                    file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name,
+                    file("${params.outdir}/salmon/WT_REP2/quant.sf").name
+                ).match("salmon_quant") },
+                { assert snapshot(
+                    path("${params.outdir}/salmon/tx2gene.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name,
+                    file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name
+                ).match("salmon") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_rsem/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_rsem/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name,
+                    file("${params.outdir}/star_rsem/bigwig/WT_REP1.forward.bigWig").name,
+                    file("${params.outdir}/star_rsem/bigwig/WT_REP1.reverse.bigWig").name,
+                    file("${params.outdir}/star_rsem/bigwig/WT_REP2.forward.bigWig").name,
+                    file("${params.outdir}/star_rsem/bigwig/WT_REP2.reverse.bigWig").name
+                ).match("star_rsem/bigwig") },
+                { assert snapshot(
+                    path("${params.outdir}/star_rsem/deseq2_qc/R_sessionInfo.log"),
+                    // These files are not stable
+                    file("${params.outdir}/star_rsem/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name,
+                    file("${params.outdir}/star_rsem/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name,
+                    file("${params.outdir}/star_rsem/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name,
+                    file("${params.outdir}/star_rsem/deseq2_qc/size_factors/WT_REP1.txt").name,
+                    file("${params.outdir}/star_rsem/deseq2_qc/size_factors/WT_REP2.txt").name,
+                    file("${params.outdir}/star_rsem/deseq2_qc/size_factors/deseq2.size_factors.RData").name,
+                    file("${params.outdir}/star_rsem/deseq2_qc/deseq2.dds.RData").name,
+                    file("${params.outdir}/star_rsem/deseq2_qc/deseq2.pca.vals.txt").name,
+                    file("${params.outdir}/star_rsem/deseq2_qc/deseq2.plots.pdf").name,
+                    file("${params.outdir}/star_rsem/deseq2_qc/deseq2.sample.dists.txt").name
+                ).match("star_rsem/deseq2_qc") },
+                { assert snapshot(
+                    path("${params.outdir}/star_rsem/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_rsem/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_rsem/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_rsem/dupradar/gene_data/WT_REP1_dupMatrix.txt"),
+                    path("${params.outdir}/star_rsem/dupradar/gene_data/WT_REP2_dupMatrix.txt"),
+                    path("${params.outdir}/star_rsem/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_rsem/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_rsem/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"),
+                    path("${params.outdir}/star_rsem/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"),
+                    path("${params.outdir}/star_rsem/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"),
+                    // PDFs are not stable
+                    file("${params.outdir}/star_rsem/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/histogram/WT_REP1_expressionHist.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/histogram/WT_REP2_expressionHist.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name,
+                    file("${params.outdir}/star_rsem/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name
+                ).match("star_rsem/dupradar") },
+                { assert snapshot(
+                    path("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"),
+                    path("${params.outdir}/star_rsem/featurecounts/WT_REP1.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/WT_REP1.featureCounts.txt"),
+                    path("${params.outdir}/star_rsem/featurecounts/WT_REP2.biotype_counts_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"),
+                    path("${params.outdir}/star_rsem/featurecounts/WT_REP2.featureCounts.txt"),
+                    // These files are unstable
+                    file("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_rsem/featurecounts/WT_REP1.featureCounts.txt.summary").name,
+                    file("${params.outdir}/star_rsem/featurecounts/WT_REP2.featureCounts.txt.summary").name
+                ).match("star_rsem/featurecounts") },
+                { assert snapshot(
+                    // These files are unstable
+                    file("${params.outdir}/star_rsem/log/RAP1_IAA_30M_REP1.log").name,
+                    file("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP1.log").name,
+                    file("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP2.log").name,
+                    file("${params.outdir}/star_rsem/log/WT_REP1.log").name,
+                    file("${params.outdir}/star_rsem/log/WT_REP2.log").name
+                ).match("star_rsem/log") },
+                { assert snapshot(
+                    // Metrics are not stable
+                    file("${params.outdir}/star_rsem/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_rsem/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_rsem/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_rsem/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name,
+                    file("${params.outdir}/star_rsem/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name
+                ).match("star_rsem/picard_metrics") },
+                { assert snapshot(
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"),
+                    path("${params.outdir}/star_rsem/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"),
+                    // HTML reports and these files are not stable
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/WT_REP1/qualimapReport.html").name,
+                    file("${params.outdir}/star_rsem/qualimap/WT_REP1/rnaseq_qc_results.txt").name,
+                    file("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name,
+                    file("${params.outdir}/star_rsem/qualimap/WT_REP2/qualimapReport.html").name,
+                    file("${params.outdir}/star_rsem/qualimap/WT_REP2/rnaseq_qc_results.txt").name
+                ).match("star_rsem/qualimap") },
+                { assert snapshot(
+                    path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.genes.results"),
+                    path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.isoforms.results"),
+                    path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.genes.results"),
+                    path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.isoforms.results"),
+                    path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.genes.results"),
+                    path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.isoforms.results"),
+                    path("${params.outdir}/star_rsem/WT_REP1.genes.results"),
+                    path("${params.outdir}/star_rsem/WT_REP1.isoforms.results"),
+                    path("${params.outdir}/star_rsem/WT_REP2.genes.results"),
+                    path("${params.outdir}/star_rsem/WT_REP2.isoforms.results"),
+                    path("${params.outdir}/star_rsem/rsem.merged.gene_counts.tsv"),
+                    path("${params.outdir}/star_rsem/rsem.merged.gene_tpm.tsv"),
+                    path("${params.outdir}/star_rsem/rsem.merged.transcript_counts.tsv"),
+                    path("${params.outdir}/star_rsem/rsem.merged.transcript_tpm.tsv"),
+                    // These files are not stable
+                    file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.cnt").name,
+                    file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.model").name,
+                    file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.theta").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.cnt").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.model").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.theta").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.cnt").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.model").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.theta").name,
+                    file("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.cnt").name,
+                    file("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.model").name,
+                    file("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.theta").name,
+                    file("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.cnt").name,
+                    file("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.model").name,
+                    file("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.theta").name
+                ).match("star_rsem/rsem") },
+                { assert snapshot(
+                    path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"),
+                    path("${params.outdir}/star_rsem/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"),
+                    path("${params.outdir}/star_rsem/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"),
+                    // PDFs, R scripts and all these files are not stable
+                    file("${params.outdir}/star_rsem/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/bam_stat/WT_REP1.bam_stat.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/bam_stat/WT_REP2.bam_stat.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_distribution/WT_REP1.read_distribution.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_distribution/WT_REP2.read_distribution.txt").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name,
+                    file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name
+                ).match("star_rsem/rseqc") },
+                { assert snapshot(
+                    // These files are not stable
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.stats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.flagstat").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.idxstats").name,
+                    file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.stats").name
+                ).match("star_rsem/samtools_stats") },
+                { assert snapshot(
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/i_data.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/e2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/e_data.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/i2t.ctab"),
+                    path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/i_data.ctab"),
+                    // These files are not stable
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name,
+                    file("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_rsem/stringtie/WT_REP1.coverage.gtf").name,
+                    file("${params.outdir}/star_rsem/stringtie/WT_REP1.gene.abundance.txt").name,
+                    file("${params.outdir}/star_rsem/stringtie/WT_REP1.transcripts.gtf").name,
+                    file("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/t_data.ctab").name,
+                    file("${params.outdir}/star_rsem/stringtie/WT_REP2.coverage.gtf").name,
+                    file("${params.outdir}/star_rsem/stringtie/WT_REP2.gene.abundance.txt").name,
+                    file("${params.outdir}/star_rsem/stringtie/WT_REP2.transcripts.gtf").name
+                ).match("star_rsem/stringtie") },
+                { assert snapshot(
+                    file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_rsem/WT_REP1.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_rsem/WT_REP1.markdup.sorted.bam.bai").name,
+                    file("${params.outdir}/star_rsem/WT_REP2.markdup.sorted.bam").name,
+                    file("${params.outdir}/star_rsem/WT_REP2.markdup.sorted.bam.bai").name
+                ).match("star_rsem/markdup") },
+                { assert snapshot(
+                    // These reports are not stable
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match("trimgalore") },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")
+                ).match("versions") }
+            )
+        }
+    }
+
+    test("Params: --aligner star_rsem - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = 'star_rsem'
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    file("${params.outdir}/custom/out/genome_transcriptome.fasta").name,
+                    file("${params.outdir}/custom/out/genome_transcriptome.gtf").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name,
+                    file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name,
+                    file("${params.outdir}/multiqc/star_rsem/multiqc_report.html").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name,
+                    file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name
+                ).match() }
+            )
+        }
+    }
+}
+
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
new file mode 100644
index 000000000..945d18f11
--- /dev/null
+++ b/tests/star_rsem.nf.test.snap
@@ -0,0 +1,1029 @@
+{
+    "star_rsem/bigwig": {
+        "content": [
+            "RAP1_IAA_30M_REP1.forward.bigWig",
+            "RAP1_IAA_30M_REP1.reverse.bigWig",
+            "RAP1_UNINDUCED_REP1.forward.bigWig",
+            "RAP1_UNINDUCED_REP1.reverse.bigWig",
+            "RAP1_UNINDUCED_REP2.forward.bigWig",
+            "RAP1_UNINDUCED_REP2.reverse.bigWig",
+            "WT_REP1.forward.bigWig",
+            "WT_REP1.reverse.bigWig",
+            "WT_REP2.forward.bigWig",
+            "WT_REP2.reverse.bigWig"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T17:25:04.845767"
+    },
+    "star_rsem/dupradar": {
+        "content": [
+            "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8da31020df3c5b25167345609c6d08c5",
+            "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,3f269a6b2e9c8eaab66582e31d208dfc",
+            "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,7d96d6ddf1d12d43837b105865aeaafa",
+            "WT_REP1_dupMatrix.txt:md5,802dd0de10d9118943869239f8659c78",
+            "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4",
+            "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,d280fe126a5e82d24121d8662fd5a161",
+            "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a498640b0f9e710311ebc3eb67cedbd0",
+            "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,a1c5346e3bad40546c793b8914a22e7e",
+            "WT_REP1_intercept_slope.txt:md5,9c2e2b7890427e79c97e65827102d965",
+            "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c",
+            "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf",
+            "WT_REP1_duprateExpBoxplot.pdf",
+            "WT_REP2_duprateExpBoxplot.pdf",
+            "RAP1_IAA_30M_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP1_expressionHist.pdf",
+            "RAP1_UNINDUCED_REP2_expressionHist.pdf",
+            "WT_REP1_expressionHist.pdf",
+            "WT_REP2_expressionHist.pdf",
+            "RAP1_IAA_30M_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP1_duprateExpDens.pdf",
+            "RAP1_UNINDUCED_REP2_duprateExpDens.pdf",
+            "WT_REP1_duprateExpDens.pdf",
+            "WT_REP2_duprateExpDens.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T17:25:05.410414"
+    },
+    "multiqc_data": {
+        "content": [
+            "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+            "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
+            "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+            "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+            "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+            "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+            "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+            "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e",
+            "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+            "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+            "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
+            "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+            "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+            "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
+            "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
+            "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+            "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
+            "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c",
+            "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c",
+            "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
+            "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
+            "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+            "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb",
+            "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
+            "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
+            "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+            "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8",
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+            "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T17:25:06.704746"
+    },
+    "fastqc/trim": {
+        "content": [
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html",
+            "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html",
+            "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip",
+            "WT_REP1_trimmed_1_val_1_fastqc.html",
+            "WT_REP1_trimmed_1_val_1_fastqc.zip",
+            "WT_REP1_trimmed_2_val_2_fastqc.html",
+            "WT_REP1_trimmed_2_val_2_fastqc.zip",
+            "WT_REP2_trimmed_1_val_1_fastqc.html",
+            "WT_REP2_trimmed_1_val_1_fastqc.zip",
+            "WT_REP2_trimmed_2_val_2_fastqc.html",
+            "WT_REP2_trimmed_2_val_2_fastqc.zip"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T17:25:04.017077"
+    },
+    "star_rsem/featurecounts": {
+        "content": [
+            "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,e66cd2b584d970ae3827ad2521f795ca",
+            "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
+            "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b3013c797d2fd38a8efa39047f5ba1b1",
+            "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,548023e639f8eb76f973a2f98bcbc82c",
+            "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb",
+            "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,ff59317794fc04d5a4fd18797f0ecb0f",
+            "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,2c0b5696582493f7a50259679982a6b3",
+            "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0",
+            "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,6ee84531ba255791a11b487b6aea75ab",
+            "WT_REP1.biotype_counts_mqc.tsv:md5,512645a8f736eee160c4465e1940f4a5",
+            "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9",
+            "WT_REP1.featureCounts.txt:md5,289cc95971a3ec550e018659279c1f59",
+            "WT_REP2.biotype_counts_mqc.tsv:md5,d4957c0197636b68d27fbd60d388bba1",
+            "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481",
+            "WT_REP2.featureCounts.txt:md5,152d2f26df56a88fe4b27c742d8f7447",
+            "RAP1_IAA_30M_REP1.featureCounts.txt.summary",
+            "RAP1_UNINDUCED_REP1.featureCounts.txt.summary",
+            "RAP1_UNINDUCED_REP2.featureCounts.txt.summary",
+            "WT_REP1.featureCounts.txt.summary",
+            "WT_REP2.featureCounts.txt.summary"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T17:25:05.539329"
+    },
+    "star_rsem/deseq2_qc": {
+        "content": [
+            "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
+            "RAP1_IAA_30M_REP1.txt",
+            "RAP1_UNINDUCED_REP1.txt",
+            "RAP1_UNINDUCED_REP2.txt",
+            "WT_REP1.txt",
+            "WT_REP2.txt",
+            "deseq2.size_factors.RData",
+            "deseq2.dds.RData",
+            "deseq2.pca.vals.txt",
+            "deseq2.plots.pdf",
+            "deseq2.sample.dists.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T17:25:05.195993"
+    },
+    "bbsplit": {
+        "content": [
+            "RAP1_IAA_30M_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP2.stats.txt",
+            "WT_REP1.stats.txt",
+            "WT_REP2.stats.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T17:25:03.953274"
+    },
+    "salmon_quant": {
+        "content": [
+            "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c",
+            "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1",
+            "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636",
+            "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935",
+            "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326",
+            "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3",
+            "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d",
+            "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6",
+            "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f",
+            "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
+            "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
+            "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac",
+            "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf",
+            "fld.gz",
+            "meta_info.json",
+            "flenDist.txt",
+            "salmon_quant.log",
+            "quant.genes.sf",
+            "quant.sf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T17:25:04.459744"
+    },
+    "star_rsem/qualimap": {
+        "content": [
+            "Coverage Profile Along Genes (High).png:md5,55ed67cd9df6d42446a76f49f6e9d6c0",
+            "Coverage Profile Along Genes (Low).png:md5,cc6887aedf7b0ce65af934849ada52f7",
+            "Coverage Profile Along Genes (Total).png:md5,ebb7199f5b5c179b3d0ad66b1833d5f0",
+            "Transcript coverage histogram.png:md5,db451ddb02fa59b2e46a3b7f936dc7e4",
+            "coverage_profile_along_genes_(high).txt:md5,31ab137e75752225365bd3d89143dbd2",
+            "coverage_profile_along_genes_(low).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1",
+            "coverage_profile_along_genes_(total).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1",
+            "Coverage Profile Along Genes (High).png:md5,36376d7393575a03f6e7a1c5be4f8c32",
+            "Coverage Profile Along Genes (Low).png:md5,24e1862606452bc53f928ccf086e3699",
+            "Coverage Profile Along Genes (Total).png:md5,c843e9063c3b15e4de1c0b3f680746a9",
+            "Transcript coverage histogram.png:md5,519b1b92340d1541d864e56b9a6956e0",
+            "coverage_profile_along_genes_(high).txt:md5,93822686a53dd40d3ff426ddbfc9314e",
+            "coverage_profile_along_genes_(low).txt:md5,bd8d58c757e4122caee4b4e8df2f4b00",
+            "coverage_profile_along_genes_(total).txt:md5,bd8d58c757e4122caee4b4e8df2f4b00",
+            "Coverage Profile Along Genes (High).png:md5,69dfa9f3eeac16a5615a4346c1d79eab",
+            "Coverage Profile Along Genes (Low).png:md5,84776e58e5aadee6be3b6225beccd70f",
+            "Coverage Profile Along Genes (Total).png:md5,2c0ddb2c5004d2f7a65e4814281a0836",
+            "Transcript coverage histogram.png:md5,2553413f136898302067b0a289f58241",
+            "coverage_profile_along_genes_(high).txt:md5,cdb2c00c43121e3beccd7f670b34e05e",
+            "coverage_profile_along_genes_(low).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed",
+            "coverage_profile_along_genes_(total).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed",
+            "Coverage Profile Along Genes (High).png:md5,4a4eb6c41483181ed9d67c390868026e",
+            "Coverage Profile Along Genes (Low).png:md5,332640c6bf816ddeec23d9e12070eede",
+            "Coverage Profile Along Genes (Total).png:md5,64402bed985293e66a634199b64c98f2",
+            "Transcript coverage histogram.png:md5,72df8608131b28ee5b23bdbc8c6e4891",
+            "coverage_profile_along_genes_(high).txt:md5,70c95fbc100f14911d2cc348bdff1587",
+            "coverage_profile_along_genes_(low).txt:md5,86e56ef794277bcf1e0d121a088b8581",
+            "coverage_profile_along_genes_(total).txt:md5,86e56ef794277bcf1e0d121a088b8581",
+            "Coverage Profile Along Genes (High).png:md5,8ec27bae1db26eb468ca35843e5eb557",
+            "Coverage Profile Along Genes (Low).png:md5,5bed9f6b9e27ad01f60d188f24020c6e",
+            "Coverage Profile Along Genes (Total).png:md5,bb10036285f9e01ed64048597a25766f",
+            "Transcript coverage histogram.png:md5,e36d2e717f852cc69f2658e6a901a0ec",
+            "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b",
+            "coverage_profile_along_genes_(low).txt:md5,7adc228bc15e344abb7938ea4d35a846",
+            "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt",
+            "Junction Analysis.png",
+            "Reads Genomic Origin.png",
+            "qualimapReport.html",
+            "rnaseq_qc_results.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T17:25:05.907994"
+    }
+}
\ No newline at end of file
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
deleted file mode 100755
index 9250125dc..000000000
--- a/workflows/rnaseq.nf
+++ /dev/null
@@ -1,941 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    PRINT PARAMS SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-def summary_params = paramsSummaryMap(workflow)
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    VALIDATE INPUTS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-WorkflowRnaseq.initialise(params, log)
-
-// Check rRNA databases for sortmerna
-if (params.remove_ribo_rna) {
-    ch_ribo_db = file(params.ribo_database_manifest)
-    if (ch_ribo_db.isEmpty()) {exit 1, "File provided with --ribo_database_manifest is empty: ${ch_ribo_db.getName()}!"}
-}
-
-// Check if file with list of fastas is provided when running BBSplit
-if (!params.skip_bbsplit && !params.bbsplit_index && params.bbsplit_fasta_list) {
-    ch_bbsplit_fasta_list = file(params.bbsplit_fasta_list)
-    if (ch_bbsplit_fasta_list.isEmpty()) {exit 1, "File provided with --bbsplit_fasta_list is empty: ${ch_bbsplit_fasta_list.getName()}!"}
-}
-
-// Check alignment parameters
-def prepareToolIndices  = []
-if (!params.skip_bbsplit) { prepareToolIndices << 'bbsplit' }
-if (!params.skip_alignment) { prepareToolIndices << params.aligner }
-if (!params.skip_pseudo_alignment && params.pseudo_aligner) { prepareToolIndices << params.pseudo_aligner }
-
-// Determine whether to filter the GTF or not
-def filterGtf = 
-    ((
-        // Condition 1: Alignment is required and aligner is set
-        !params.skip_alignment && params.aligner
-    ) || 
-    (
-        // Condition 2: Pseudoalignment is required and pseudoaligner is set
-        !params.skip_pseudo_alignment && params.pseudo_aligner
-    ) || 
-    (
-        // Condition 3: Transcript FASTA file is not provided
-        !params.transcript_fasta
-    )) &&
-    (
-        // Condition 4: --skip_gtf_filter is not provided
-        !params.skip_gtf_filter
-    )
-
-// Get RSeqC modules to run
-def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
-if (params.bam_csi_index) {
-    for (rseqc_module in ['read_distribution', 'inner_distance', 'tin']) {
-        if (rseqc_modules.contains(rseqc_module)) {
-            rseqc_modules.remove(rseqc_module)
-        }
-    }
-}
-
-// Stage dummy file to be used as an optional input where required
-ch_dummy_file = file("$projectDir/assets/dummy_file.txt", checkIfExists: true)
-
-// Check if an AWS iGenome has been provided to use the appropriate version of STAR
-def is_aws_igenome = false
-if (params.fasta && params.gtf) {
-    if ((file(params.fasta).getName() - '.gz' == 'genome.fa') && (file(params.gtf).getName() - '.gz' == 'genes.gtf')) {
-        is_aws_igenome = true
-    }
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
-ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath(params.multiqc_logo)   : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-
-// Header files for MultiQC
-ch_pca_header_multiqc        = file("$projectDir/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true)
-ch_clustering_header_multiqc = file("$projectDir/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true)
-ch_biotypes_header_multiqc   = file("$projectDir/assets/multiqc/biotypes_header.txt", checkIfExists: true)
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT LOCAL MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// MODULE: Loaded from modules/local/
-//
-include { BEDTOOLS_GENOMECOV                 } from '../modules/local/bedtools_genomecov'
-include { DESEQ2_QC as DESEQ2_QC_STAR_SALMON } from '../modules/local/deseq2_qc'
-include { DESEQ2_QC as DESEQ2_QC_RSEM        } from '../modules/local/deseq2_qc'
-include { DESEQ2_QC as DESEQ2_QC_PSEUDO      } from '../modules/local/deseq2_qc'
-include { DUPRADAR                           } from '../modules/local/dupradar'
-include { MULTIQC                            } from '../modules/local/multiqc'
-include { MULTIQC_CUSTOM_BIOTYPE             } from '../modules/local/multiqc_custom_biotype'
-include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../modules/local/umitools_prepareforrsem'
-
-//
-// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
-//
-include { PREPARE_GENOME                                    } from '../subworkflows/local/prepare_genome'
-include { ALIGN_STAR                                        } from '../subworkflows/local/align_star'
-include { QUANTIFY_RSEM                                     } from '../subworkflows/local/quantify_rsem'
-include { QUANTIFY_PSEUDO_ALIGNMENT as QUANTIFY_STAR_SALMON } from '../subworkflows/local/quantify_pseudo'
-include { QUANTIFY_PSEUDO_ALIGNMENT                         } from '../subworkflows/local/quantify_pseudo'
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// MODULE: Installed directly from nf-core/modules
-//
-include { CAT_FASTQ                   } from '../modules/nf-core/cat/fastq'
-include { BBMAP_BBSPLIT               } from '../modules/nf-core/bbmap/bbsplit'
-include { SAMTOOLS_SORT               } from '../modules/nf-core/samtools/sort'
-include { PRESEQ_LCEXTRAP             } from '../modules/nf-core/preseq/lcextrap'
-include { QUALIMAP_RNASEQ             } from '../modules/nf-core/qualimap/rnaseq'
-include { SORTMERNA                   } from '../modules/nf-core/sortmerna'
-include { STRINGTIE_STRINGTIE         } from '../modules/nf-core/stringtie/stringtie'
-include { SUBREAD_FEATURECOUNTS       } from '../modules/nf-core/subread/featurecounts'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions'
-
-//
-// SUBWORKFLOW: Consisting entirely of nf-core/modules
-//
-include { FASTQ_SUBSAMPLE_FQ_SALMON        } from '../subworkflows/nf-core/fastq_subsample_fq_salmon'
-include { FASTQ_FASTQC_UMITOOLS_TRIMGALORE } from '../subworkflows/nf-core/fastq_fastqc_umitools_trimgalore'
-include { FASTQ_FASTQC_UMITOOLS_FASTP      } from '../subworkflows/nf-core/fastq_fastqc_umitools_fastp'
-include { FASTQ_ALIGN_HISAT2               } from '../subworkflows/nf-core/fastq_align_hisat2'
-include { BAM_SORT_STATS_SAMTOOLS          } from '../subworkflows/nf-core/bam_sort_stats_samtools'
-include { BAM_MARKDUPLICATES_PICARD        } from '../subworkflows/nf-core/bam_markduplicates_picard'
-include { BAM_RSEQC                        } from '../subworkflows/nf-core/bam_rseqc'
-include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME        } from '../subworkflows/nf-core/bam_dedup_stats_samtools_umitools'
-include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME } from '../subworkflows/nf-core/bam_dedup_stats_samtools_umitools'
-include { BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG as BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD } from '../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig'
-include { BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG as BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE } from '../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig'
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN MAIN WORKFLOW
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-// Info required for completion email and summary
-def multiqc_report     = []
-def pass_mapped_reads  = [:]
-def pass_trimmed_reads = [:]
-def pass_strand_check  = [:]
-
-workflow RNASEQ {
-
-    ch_versions = Channel.empty()
-
-    //
-    // SUBWORKFLOW: Uncompress and prepare reference genome files
-    //
-    def biotype = params.gencode ? "gene_type" : params.featurecounts_group_type
-    PREPARE_GENOME (
-        params.fasta,
-        params.gtf,
-        params.gff,
-        params.additional_fasta,
-        params.transcript_fasta,
-        params.gene_bed,
-        params.splicesites,
-        params.bbsplit_fasta_list,
-        params.star_index,
-        params.rsem_index,
-        params.salmon_index,
-        params.kallisto_index,
-        params.hisat2_index,
-        params.bbsplit_index,
-        params.gencode,
-        is_aws_igenome,
-        biotype,
-        prepareToolIndices,
-        filterGtf
-    )
-    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
-
-    // Check if contigs in genome fasta file > 512 Mbp
-    if (!params.skip_alignment && !params.bam_csi_index) {
-        PREPARE_GENOME
-            .out
-            .fai
-            .map { WorkflowRnaseq.checkMaxContigSize(it, log) }
-    }
-
-    //
-    // Create input channel from input file provided through params.input
-    //
-    Channel
-        .fromSamplesheet("input")
-        .map {
-            meta, fastq_1, fastq_2 ->
-                if (!fastq_2) {
-                    return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
-                } else {
-                    return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
-                }
-        }
-        .groupTuple()
-        .map {
-            WorkflowRnaseq.validateInput(it)
-        }
-        .branch {
-            meta, fastqs ->
-                single  : fastqs.size() == 1
-                    return [ meta, fastqs.flatten() ]
-                multiple: fastqs.size() > 1
-                    return [ meta, fastqs.flatten() ]
-        }
-        .set { ch_fastq }
-
-    //
-    // MODULE: Concatenate FastQ files from same sample if required
-    //
-    CAT_FASTQ (
-        ch_fastq.multiple
-    )
-    .reads
-    .mix(ch_fastq.single)
-    .set { ch_cat_fastq }
-    ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null))
-
-    //
-    // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore!
-    //
-    ch_filtered_reads      = Channel.empty()
-    ch_fastqc_raw_multiqc  = Channel.empty()
-    ch_fastqc_trim_multiqc = Channel.empty()
-    ch_trim_log_multiqc    = Channel.empty()
-    ch_trim_read_count     = Channel.empty()
-    if (params.trimmer == 'trimgalore') {
-        FASTQ_FASTQC_UMITOOLS_TRIMGALORE (
-            ch_cat_fastq,
-            params.skip_fastqc || params.skip_qc,
-            params.with_umi,
-            params.skip_umi_extract,
-            params.skip_trimming,
-            params.umi_discard_read,
-            params.min_trimmed_reads
-        )
-        ch_filtered_reads      = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.reads
-        ch_fastqc_raw_multiqc  = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.fastqc_zip
-        ch_fastqc_trim_multiqc = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_zip
-        ch_trim_log_multiqc    = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log
-        ch_trim_read_count     = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_read_count
-        ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.versions)
-    }
-
-    //
-    // SUBWORKFLOW: Read QC, extract UMI and trim adapters with fastp
-    //
-    if (params.trimmer == 'fastp') {
-        FASTQ_FASTQC_UMITOOLS_FASTP (
-            ch_cat_fastq,
-            params.skip_fastqc || params.skip_qc,
-            params.with_umi,
-            params.skip_umi_extract,
-            params.umi_discard_read,
-            params.skip_trimming,
-            [],
-            params.save_trimmed,
-            params.save_trimmed,
-            params.min_trimmed_reads
-        )
-        ch_filtered_reads      = FASTQ_FASTQC_UMITOOLS_FASTP.out.reads
-        ch_fastqc_raw_multiqc  = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip
-        ch_fastqc_trim_multiqc = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip
-        ch_trim_log_multiqc    = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json
-        ch_trim_read_count     = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_read_count
-        ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.versions)
-    }
-
-    //
-    // Get list of samples that failed trimming threshold for MultiQC report
-    //
-    ch_trim_read_count
-        .map {
-            meta, num_reads ->
-                pass_trimmed_reads[meta.id] = true
-                if (num_reads <= params.min_trimmed_reads.toFloat()) {
-                    pass_trimmed_reads[meta.id] = false
-                    return [ "$meta.id\t$num_reads" ]
-                }
-        }
-        .collect()
-        .map {
-            tsv_data ->
-                def header = ["Sample", "Reads after trimming"]
-                WorkflowRnaseq.multiqcTsvFromList(tsv_data, header)
-        }
-        .set { ch_fail_trimming_multiqc }
-
-    //
-    // MODULE: Remove genome contaminant reads
-    //
-    if (!params.skip_bbsplit) {
-        BBMAP_BBSPLIT (
-            ch_filtered_reads,
-            PREPARE_GENOME.out.bbsplit_index,
-            [],
-            [ [], [] ],
-            false
-        )
-        .primary_fastq
-        .set { ch_filtered_reads }
-        ch_versions = ch_versions.mix(BBMAP_BBSPLIT.out.versions.first())
-    }
-
-    //
-    // MODULE: Remove ribosomal RNA reads
-    //
-    ch_sortmerna_multiqc = Channel.empty()
-    if (params.remove_ribo_rna) {
-        ch_sortmerna_fastas = Channel.from(ch_ribo_db.readLines()).map { row -> file(row, checkIfExists: true) }.collect()
-
-        SORTMERNA (
-            ch_filtered_reads,
-            ch_sortmerna_fastas
-        )
-        .reads
-        .set { ch_filtered_reads }
-
-        ch_sortmerna_multiqc = SORTMERNA.out.log
-        ch_versions = ch_versions.mix(SORTMERNA.out.versions.first())
-    }
-    
-    //
-    // SUBWORKFLOW: Sub-sample FastQ files and pseudoalign with Salmon to auto-infer strandedness
-    //
-    
-    // Branch FastQ channels if 'auto' specified to infer strandedness
-    ch_filtered_reads
-        .branch {
-            meta, fastq ->
-                auto_strand : meta.strandedness == 'auto'
-                    return [ meta, fastq ]
-                known_strand: meta.strandedness != 'auto'
-                    return [ meta, fastq ]
-        }
-        .set { ch_strand_fastq }
-
-    // Return empty channel if ch_strand_fastq.auto_strand is empty so salmon index isn't created
-    PREPARE_GENOME
-        .out
-        .fasta
-        .combine(ch_strand_fastq.auto_strand)
-        .map { it.first() }
-        .first()
-        .set { ch_genome_fasta }
-
-    FASTQ_SUBSAMPLE_FQ_SALMON (
-        ch_strand_fastq.auto_strand,
-        ch_genome_fasta,
-        PREPARE_GENOME.out.transcript_fasta,
-        PREPARE_GENOME.out.gtf,
-        PREPARE_GENOME.out.salmon_index,
-        !params.salmon_index && !('salmon' in prepareToolIndices)
-    )
-    ch_versions = ch_versions.mix(FASTQ_SUBSAMPLE_FQ_SALMON.out.versions)
-
-    FASTQ_SUBSAMPLE_FQ_SALMON
-        .out
-        .json_info
-        .join(ch_strand_fastq.auto_strand)
-        .map { meta, json, reads ->
-            return [ meta + [ strandedness: WorkflowRnaseq.getSalmonInferredStrandedness(json) ], reads ]
-        }
-        .mix(ch_strand_fastq.known_strand)
-        .set { ch_strand_inferred_filtered_fastq }
-
-    //
-    // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with Salmon
-    //
-    ch_genome_bam                 = Channel.empty()
-    ch_genome_bam_index           = Channel.empty()
-    ch_samtools_stats             = Channel.empty()
-    ch_samtools_flagstat          = Channel.empty()
-    ch_samtools_idxstats          = Channel.empty()
-    ch_star_multiqc               = Channel.empty()
-    ch_aligner_pca_multiqc        = Channel.empty()
-    ch_aligner_clustering_multiqc = Channel.empty()
-    if (!params.skip_alignment && params.aligner == 'star_salmon') {
-        ALIGN_STAR (
-            ch_strand_inferred_filtered_fastq,
-            PREPARE_GENOME.out.star_index.map { [ [:], it ] },
-            PREPARE_GENOME.out.gtf.map { [ [:], it ] },
-            params.star_ignore_sjdbgtf,
-            '',
-            params.seq_center ?: '',
-            is_aws_igenome,
-            PREPARE_GENOME.out.fasta.map { [ [:], it ] }
-        )
-        ch_genome_bam        = ALIGN_STAR.out.bam
-        ch_genome_bam_index  = ALIGN_STAR.out.bai
-        ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript
-        ch_samtools_stats    = ALIGN_STAR.out.stats
-        ch_samtools_flagstat = ALIGN_STAR.out.flagstat
-        ch_samtools_idxstats = ALIGN_STAR.out.idxstats
-        ch_star_multiqc      = ALIGN_STAR.out.log_final
-        if (params.bam_csi_index) {
-            ch_genome_bam_index = ALIGN_STAR.out.csi
-        }
-        ch_versions = ch_versions.mix(ALIGN_STAR.out.versions)
-
-        //
-        // SUBWORKFLOW: Remove duplicate reads from BAM file based on UMIs
-        //
-        if (params.with_umi) {
-            // Deduplicate genome BAM file before downstream analysis
-            BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME (
-                ch_genome_bam.join(ch_genome_bam_index, by: [0]),
-                params.umitools_dedup_stats
-            )
-            ch_genome_bam        = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bam
-            ch_genome_bam_index  = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bai
-            ch_samtools_stats    = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.stats
-            ch_samtools_flagstat = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.flagstat
-            ch_samtools_idxstats = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.idxstats
-            if (params.bam_csi_index) {
-                ch_genome_bam_index  = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.csi
-            }
-            ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.versions)
-
-            // Co-ordinate sort, index and run stats on transcriptome BAM
-            BAM_SORT_STATS_SAMTOOLS (
-                ch_transcriptome_bam,
-                PREPARE_GENOME.out.fasta.map { [ [:], it ] }
-            )
-            ch_transcriptome_sorted_bam = BAM_SORT_STATS_SAMTOOLS.out.bam
-            ch_transcriptome_sorted_bai = BAM_SORT_STATS_SAMTOOLS.out.bai
-
-            // Deduplicate transcriptome BAM file before read counting with Salmon
-            BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME (
-                ch_transcriptome_sorted_bam.join(ch_transcriptome_sorted_bai, by: [0]),
-                params.umitools_dedup_stats
-            )
-
-            // Name sort BAM before passing to Salmon
-            SAMTOOLS_SORT (
-                BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bam
-            )
-
-            // Only run prepare_for_rsem.py on paired-end BAM files
-            SAMTOOLS_SORT
-                .out
-                .bam
-                .branch {
-                    meta, bam ->
-                        single_end: meta.single_end
-                            return [ meta, bam ]
-                        paired_end: !meta.single_end
-                            return [ meta, bam ]
-                }
-                .set { ch_umitools_dedup_bam }
-
-            // Fix paired-end reads in name sorted BAM file
-            // See: https://github.com/nf-core/rnaseq/issues/828
-            UMITOOLS_PREPAREFORSALMON (
-                ch_umitools_dedup_bam.paired_end
-            )
-            ch_versions = ch_versions.mix(UMITOOLS_PREPAREFORSALMON.out.versions.first())
-
-            ch_umitools_dedup_bam
-                .single_end
-                .mix(UMITOOLS_PREPAREFORSALMON.out.bam)
-                .set { ch_transcriptome_bam }
-        }
-
-        //
-        // SUBWORKFLOW: Count reads from BAM alignments using Salmon
-        //
-        QUANTIFY_STAR_SALMON (
-            ch_transcriptome_bam,
-            ch_dummy_file,
-            PREPARE_GENOME.out.transcript_fasta,
-            PREPARE_GENOME.out.gtf,
-            'salmon',
-            true,
-            params.salmon_quant_libtype ?: '',
-            params.kallisto_quant_fraglen,
-            params.kallisto_quant_fraglen_sd
-        )
-        ch_versions = ch_versions.mix(QUANTIFY_STAR_SALMON.out.versions)
-
-        if (!params.skip_qc & !params.skip_deseq2_qc) {
-            DESEQ2_QC_STAR_SALMON (
-                QUANTIFY_STAR_SALMON.out.counts_gene_length_scaled,
-                ch_pca_header_multiqc,
-                ch_clustering_header_multiqc
-            )
-            ch_aligner_pca_multiqc        = DESEQ2_QC_STAR_SALMON.out.pca_multiqc
-            ch_aligner_clustering_multiqc = DESEQ2_QC_STAR_SALMON.out.dists_multiqc
-            ch_versions = ch_versions.mix(DESEQ2_QC_STAR_SALMON.out.versions)
-        }
-    }
-
-    //
-    // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with RSEM
-    //
-    ch_rsem_multiqc = Channel.empty()
-    if (!params.skip_alignment && params.aligner == 'star_rsem') {
-        QUANTIFY_RSEM (
-            ch_strand_inferred_filtered_fastq,
-            PREPARE_GENOME.out.rsem_index,
-            PREPARE_GENOME.out.fasta.map { [ [:], it ] }
-        )
-        ch_genome_bam        = QUANTIFY_RSEM.out.bam
-        ch_genome_bam_index  = QUANTIFY_RSEM.out.bai
-        ch_samtools_stats    = QUANTIFY_RSEM.out.stats
-        ch_samtools_flagstat = QUANTIFY_RSEM.out.flagstat
-        ch_samtools_idxstats = QUANTIFY_RSEM.out.idxstats
-        ch_star_multiqc      = QUANTIFY_RSEM.out.logs
-        ch_rsem_multiqc      = QUANTIFY_RSEM.out.stat
-        if (params.bam_csi_index) {
-            ch_genome_bam_index = QUANTIFY_RSEM.out.csi
-        }
-        ch_versions = ch_versions.mix(QUANTIFY_RSEM.out.versions)
-
-        if (!params.skip_qc & !params.skip_deseq2_qc) {
-            DESEQ2_QC_RSEM (
-                QUANTIFY_RSEM.out.merged_counts_gene,
-                ch_pca_header_multiqc,
-                ch_clustering_header_multiqc
-            )
-            ch_aligner_pca_multiqc        = DESEQ2_QC_RSEM.out.pca_multiqc
-            ch_aligner_clustering_multiqc = DESEQ2_QC_RSEM.out.dists_multiqc
-            ch_versions = ch_versions.mix(DESEQ2_QC_RSEM.out.versions)
-        }
-    }
-
-    //
-    // SUBWORKFLOW: Alignment with HISAT2
-    //
-    ch_hisat2_multiqc = Channel.empty()
-    if (!params.skip_alignment && params.aligner == 'hisat2') {
-        FASTQ_ALIGN_HISAT2 (
-            ch_strand_inferred_filtered_fastq,
-            PREPARE_GENOME.out.hisat2_index.map { [ [:], it ] },
-            PREPARE_GENOME.out.splicesites.map { [ [:], it ] },
-            PREPARE_GENOME.out.fasta.map { [ [:], it ] }
-        )
-        ch_genome_bam        = FASTQ_ALIGN_HISAT2.out.bam
-        ch_genome_bam_index  = FASTQ_ALIGN_HISAT2.out.bai
-        ch_samtools_stats    = FASTQ_ALIGN_HISAT2.out.stats
-        ch_samtools_flagstat = FASTQ_ALIGN_HISAT2.out.flagstat
-        ch_samtools_idxstats = FASTQ_ALIGN_HISAT2.out.idxstats
-        ch_hisat2_multiqc    = FASTQ_ALIGN_HISAT2.out.summary
-        if (params.bam_csi_index) {
-            ch_genome_bam_index = FASTQ_ALIGN_HISAT2.out.csi
-        }
-        ch_versions = ch_versions.mix(FASTQ_ALIGN_HISAT2.out.versions)
-
-        //
-        // SUBWORKFLOW: Remove duplicate reads from BAM file based on UMIs
-        //
-        if (params.with_umi) {
-            BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME (
-                ch_genome_bam.join(ch_genome_bam_index, by: [0]),
-                params.umitools_dedup_stats
-            )
-            ch_genome_bam        = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bam
-            ch_genome_bam_index  = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bai
-            ch_samtools_stats    = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.stats
-            ch_samtools_flagstat = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.flagstat
-            ch_samtools_idxstats = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.idxstats
-            if (params.bam_csi_index) {
-                ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.csi
-            }
-            ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.versions)
-        }
-    }
-
-    //
-    // Filter channels to get samples that passed STAR minimum mapping percentage
-    //
-    ch_fail_mapping_multiqc = Channel.empty()
-    if (!params.skip_alignment && params.aligner.contains('star')) {
-        ch_star_multiqc
-            .map { meta, align_log -> [ meta ] + WorkflowRnaseq.getStarPercentMapped(params, align_log) }
-            .set { ch_percent_mapped }
-
-        ch_genome_bam
-            .join(ch_percent_mapped, by: [0])
-            .map { meta, ofile, mapped, pass -> if (pass) [ meta, ofile ] }
-            .set { ch_genome_bam }
-
-        ch_genome_bam_index
-            .join(ch_percent_mapped, by: [0])
-            .map { meta, ofile, mapped, pass -> if (pass) [ meta, ofile ] }
-            .set { ch_genome_bam_index }
-
-        ch_percent_mapped
-            .branch { meta, mapped, pass ->
-                pass: pass
-                    pass_mapped_reads[meta.id] = true
-                    return [ "$meta.id\t$mapped" ]
-                fail: !pass
-                    pass_mapped_reads[meta.id] = false
-                    return [ "$meta.id\t$mapped" ]
-            }
-            .set { ch_pass_fail_mapped }
-
-        ch_pass_fail_mapped
-            .fail
-            .collect()
-            .map {
-                tsv_data ->
-                    def header = ["Sample", "STAR uniquely mapped reads (%)"]
-                    WorkflowRnaseq.multiqcTsvFromList(tsv_data, header)
-            }
-            .set { ch_fail_mapping_multiqc }
-    }
-
-    //
-    // MODULE: Run Preseq
-    //
-    ch_preseq_multiqc = Channel.empty()
-    if (!params.skip_alignment && !params.skip_qc && !params.skip_preseq) {
-        PRESEQ_LCEXTRAP (
-            ch_genome_bam
-        )
-        ch_preseq_multiqc = PRESEQ_LCEXTRAP.out.lc_extrap
-        ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first())
-    }
-
-    //
-    // SUBWORKFLOW: Mark duplicate reads
-    //
-    ch_markduplicates_multiqc = Channel.empty()
-    if (!params.skip_alignment && !params.skip_markduplicates && !params.with_umi) {
-        BAM_MARKDUPLICATES_PICARD (
-            ch_genome_bam,
-            PREPARE_GENOME.out.fasta.map { [ [:], it ] },
-            PREPARE_GENOME.out.fai.map { [ [:], it ] }
-        )
-        ch_genome_bam             = BAM_MARKDUPLICATES_PICARD.out.bam
-        ch_genome_bam_index       = BAM_MARKDUPLICATES_PICARD.out.bai
-        ch_samtools_stats         = BAM_MARKDUPLICATES_PICARD.out.stats
-        ch_samtools_flagstat      = BAM_MARKDUPLICATES_PICARD.out.flagstat
-        ch_samtools_idxstats      = BAM_MARKDUPLICATES_PICARD.out.idxstats
-        ch_markduplicates_multiqc = BAM_MARKDUPLICATES_PICARD.out.metrics
-        if (params.bam_csi_index) {
-            ch_genome_bam_index = BAM_MARKDUPLICATES_PICARD.out.csi
-        }
-        ch_versions = ch_versions.mix(BAM_MARKDUPLICATES_PICARD.out.versions)
-    }
-
-    //
-    // MODULE: STRINGTIE
-    //
-    if (!params.skip_alignment && !params.skip_stringtie) {
-        STRINGTIE_STRINGTIE (
-            ch_genome_bam,
-            PREPARE_GENOME.out.gtf
-        )
-        ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions.first())
-    }
-
-    //
-    // MODULE: Feature biotype QC using featureCounts
-    //
-    ch_featurecounts_multiqc = Channel.empty()
-    if (!params.skip_alignment && !params.skip_qc && !params.skip_biotype_qc && biotype) {
-
-        PREPARE_GENOME
-            .out
-            .gtf
-            .map { WorkflowRnaseq.biotypeInGtf(it, biotype, log) }
-            .set { biotype_in_gtf }
-
-        // Prevent any samples from running if GTF file doesn't have a valid biotype
-        ch_genome_bam
-            .combine(PREPARE_GENOME.out.gtf)
-            .combine(biotype_in_gtf)
-            .filter { it[-1] }
-            .map { it[0..<it.size()-1] }
-            .set { ch_featurecounts }
-
-        SUBREAD_FEATURECOUNTS (
-            ch_featurecounts
-        )
-        ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS.out.versions.first())
-
-        MULTIQC_CUSTOM_BIOTYPE (
-            SUBREAD_FEATURECOUNTS.out.counts,
-            ch_biotypes_header_multiqc
-        )
-        ch_featurecounts_multiqc = MULTIQC_CUSTOM_BIOTYPE.out.tsv
-        ch_versions = ch_versions.mix(MULTIQC_CUSTOM_BIOTYPE.out.versions.first())
-    }
-
-    //
-    // MODULE: Genome-wide coverage with BEDTools
-    //
-    if (!params.skip_alignment && !params.skip_bigwig) {
-
-        BEDTOOLS_GENOMECOV (
-            ch_genome_bam
-        )
-        ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions.first())
-
-        //
-        // SUBWORKFLOW: Convert bedGraph to bigWig
-        //
-        BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD (
-            BEDTOOLS_GENOMECOV.out.bedgraph_forward,
-            PREPARE_GENOME.out.chrom_sizes
-        )
-        ch_versions = ch_versions.mix(BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD.out.versions)
-
-        BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE (
-            BEDTOOLS_GENOMECOV.out.bedgraph_reverse,
-            PREPARE_GENOME.out.chrom_sizes
-        )
-    }
-
-    //
-    // MODULE: Downstream QC steps
-    //
-    ch_qualimap_multiqc           = Channel.empty()
-    ch_dupradar_multiqc           = Channel.empty()
-    ch_bamstat_multiqc            = Channel.empty()
-    ch_inferexperiment_multiqc    = Channel.empty()
-    ch_innerdistance_multiqc      = Channel.empty()
-    ch_junctionannotation_multiqc = Channel.empty()
-    ch_junctionsaturation_multiqc = Channel.empty()
-    ch_readdistribution_multiqc   = Channel.empty()
-    ch_readduplication_multiqc    = Channel.empty()
-    ch_fail_strand_multiqc        = Channel.empty()
-    ch_tin_multiqc                = Channel.empty()
-    if (!params.skip_alignment && !params.skip_qc) {
-        if (!params.skip_qualimap) {
-            QUALIMAP_RNASEQ (
-                ch_genome_bam,
-                PREPARE_GENOME.out.gtf.map { [ [:], it ] }
-            )
-            ch_qualimap_multiqc = QUALIMAP_RNASEQ.out.results
-            ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions.first())
-        }
-
-        if (!params.skip_dupradar) {
-            DUPRADAR (
-                ch_genome_bam,
-                PREPARE_GENOME.out.gtf
-            )
-            ch_dupradar_multiqc = DUPRADAR.out.multiqc
-            ch_versions = ch_versions.mix(DUPRADAR.out.versions.first())
-        }
-
-        if (!params.skip_rseqc && rseqc_modules.size() > 0) {
-            BAM_RSEQC (
-                ch_genome_bam.join(ch_genome_bam_index, by: [0]),
-                PREPARE_GENOME.out.gene_bed,
-                rseqc_modules
-            )
-            ch_bamstat_multiqc            = BAM_RSEQC.out.bamstat_txt
-            ch_inferexperiment_multiqc    = BAM_RSEQC.out.inferexperiment_txt
-            ch_innerdistance_multiqc      = BAM_RSEQC.out.innerdistance_freq
-            ch_junctionannotation_multiqc = BAM_RSEQC.out.junctionannotation_log
-            ch_junctionsaturation_multiqc = BAM_RSEQC.out.junctionsaturation_rscript
-            ch_readdistribution_multiqc   = BAM_RSEQC.out.readdistribution_txt
-            ch_readduplication_multiqc    = BAM_RSEQC.out.readduplication_pos_xls
-            ch_tin_multiqc                = BAM_RSEQC.out.tin_txt
-            ch_versions = ch_versions.mix(BAM_RSEQC.out.versions)
-
-            ch_inferexperiment_multiqc
-                .map {
-                    meta, strand_log ->
-                        def inferred_strand = WorkflowRnaseq.getInferexperimentStrandedness(strand_log, 30)
-                        pass_strand_check[meta.id] = true
-                        if (meta.strandedness != inferred_strand[0]) {
-                            pass_strand_check[meta.id] = false
-                            return [ "$meta.id\t$meta.strandedness\t${inferred_strand.join('\t')}" ]
-                        }
-                }
-                .collect()
-                .map {
-                    tsv_data ->
-                        def header = [
-                            "Sample",
-                            "Provided strandedness",
-                            "Inferred strandedness",
-                            "Sense (%)",
-                            "Antisense (%)",
-                            "Undetermined (%)"
-                        ]
-                        WorkflowRnaseq.multiqcTsvFromList(tsv_data, header)
-                }
-                .set { ch_fail_strand_multiqc }
-        }
-    }
-
-    //
-    // SUBWORKFLOW: Pseudoalignment and quantification with Salmon
-    //
-    ch_pseudo_multiqc                   = Channel.empty()
-    ch_pseudoaligner_pca_multiqc        = Channel.empty()
-    ch_pseudoaligner_clustering_multiqc = Channel.empty()    
-    if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
-
-       if (params.pseudo_aligner == 'salmon') {
-           ch_pseudo_index = PREPARE_GENOME.out.salmon_index
-       } else {
-           ch_pseudo_index = PREPARE_GENOME.out.kallisto_index
-       }
-
-        QUANTIFY_PSEUDO_ALIGNMENT (
-            ch_strand_inferred_filtered_fastq,
-            ch_pseudo_index,
-            ch_dummy_file,
-            PREPARE_GENOME.out.gtf,
-            params.pseudo_aligner,
-            false,
-            params.salmon_quant_libtype ?: '',
-            params.kallisto_quant_fraglen,
-            params.kallisto_quant_fraglen_sd
-        )
-        ch_pseudo_multiqc            = QUANTIFY_PSEUDO_ALIGNMENT.out.multiqc
-        ch_counts_gene_length_scaled = QUANTIFY_PSEUDO_ALIGNMENT.out.counts_gene_length_scaled
-        ch_versions = ch_versions.mix(QUANTIFY_PSEUDO_ALIGNMENT.out.versions)
-
-        if (!params.skip_qc & !params.skip_deseq2_qc) {
-            DESEQ2_QC_PSEUDO (
-                ch_counts_gene_length_scaled,
-                ch_pca_header_multiqc,
-                ch_clustering_header_multiqc
-            )
-            ch_pseudoaligner_pca_multiqc        = DESEQ2_QC_PSEUDO.out.pca_multiqc
-            ch_pseudoaligner_clustering_multiqc = DESEQ2_QC_PSEUDO.out.dists_multiqc
-            ch_versions = ch_versions.mix(DESEQ2_QC_PSEUDO.out.versions)
-        }
-    }
-    
-    //
-    // MODULE: Pipeline reporting
-    //
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
-    )
-
-    //
-    // MODULE: MultiQC
-    //
-    if (!params.skip_multiqc) {
-        workflow_summary    = WorkflowRnaseq.paramsSummaryMultiqc(workflow, summary_params)
-        ch_workflow_summary = Channel.value(workflow_summary)
-
-        methods_description    = WorkflowRnaseq.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
-        ch_methods_description = Channel.value(methods_description)
-
-        MULTIQC (
-            ch_multiqc_config,
-            ch_multiqc_custom_config.collect().ifEmpty([]),
-            CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect(),
-            ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'),
-            ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'),
-            ch_multiqc_logo.collect().ifEmpty([]),
-            ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv').ifEmpty([]),
-            ch_fail_mapping_multiqc.collectFile(name: 'fail_mapped_samples_mqc.tsv').ifEmpty([]),
-            ch_fail_strand_multiqc.collectFile(name: 'fail_strand_check_mqc.tsv').ifEmpty([]),
-            ch_fastqc_raw_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_fastqc_trim_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_trim_log_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_sortmerna_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_star_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_hisat2_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_rsem_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_pseudo_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_samtools_stats.collect{it[1]}.ifEmpty([]),
-            ch_samtools_flagstat.collect{it[1]}.ifEmpty([]),
-            ch_samtools_idxstats.collect{it[1]}.ifEmpty([]),
-            ch_markduplicates_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_featurecounts_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_aligner_pca_multiqc.collect().ifEmpty([]),
-            ch_aligner_clustering_multiqc.collect().ifEmpty([]),
-            ch_pseudoaligner_pca_multiqc.collect().ifEmpty([]),
-            ch_pseudoaligner_clustering_multiqc.collect().ifEmpty([]),
-            ch_preseq_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_qualimap_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_dupradar_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_bamstat_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_inferexperiment_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_innerdistance_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_junctionannotation_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_junctionsaturation_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_readdistribution_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_readduplication_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_tin_multiqc.collect{it[1]}.ifEmpty([])
-        )
-        multiqc_report = MULTIQC.out.report.toList()
-    }
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    COMPLETION EMAIL AND SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report, pass_mapped_reads, pass_trimmed_reads, pass_strand_check)
-    }
-    
-    NfcoreTemplate.dump_parameters(workflow, params)
-    NfcoreTemplate.summary(workflow, params, log, pass_mapped_reads, pass_trimmed_reads, pass_strand_check)
-
-    if (params.hook_url) {
-        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
-    }
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
diff --git a/assets/multiqc/biotypes_header.txt b/workflows/rnaseq/assets/multiqc/biotypes_header.txt
similarity index 100%
rename from assets/multiqc/biotypes_header.txt
rename to workflows/rnaseq/assets/multiqc/biotypes_header.txt
diff --git a/assets/multiqc/deseq2_clustering_header.txt b/workflows/rnaseq/assets/multiqc/deseq2_clustering_header.txt
similarity index 72%
rename from assets/multiqc/deseq2_clustering_header.txt
rename to workflows/rnaseq/assets/multiqc/deseq2_clustering_header.txt
index 04e10efa5..f2f5dc852 100644
--- a/assets/multiqc/deseq2_clustering_header.txt
+++ b/workflows/rnaseq/assets/multiqc/deseq2_clustering_header.txt
@@ -4,9 +4,12 @@
 #	       <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html' target='_blank'>DESeq2</a>
 #              rlog values for each sample
 #              in the <a href='https://github.com/nf-core/rnaseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
+#parent_id: 'sample-relationships'
+#parent_name: 'Sample relationships'
+#parent_description: 'Plots interrogating sample relationships, based on final count matrices'
 #plot_type: 'heatmap'
 #anchor: 'deseq2_clustering'
 #pconfig:
 #    title: 'DESeq2: Heatmap of the sample-to-sample distances'
-#    xlab: True
-#    reverseColors: True
+#    xlog: True
+#    reverse_colors: True
diff --git a/assets/multiqc/deseq2_pca_header.txt b/workflows/rnaseq/assets/multiqc/deseq2_pca_header.txt
similarity index 75%
rename from assets/multiqc/deseq2_pca_header.txt
rename to workflows/rnaseq/assets/multiqc/deseq2_pca_header.txt
index 636f9374d..cb20ce49b 100644
--- a/assets/multiqc/deseq2_pca_header.txt
+++ b/workflows/rnaseq/assets/multiqc/deseq2_pca_header.txt
@@ -3,6 +3,9 @@
 #description: "PCA plot between samples in the experiment.
 #              These values are calculated using <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html'>DESeq2</a>
 #              in the <a href='https://github.com/nf-core/rnaseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
+#parent_id: 'sample-relationships'
+#parent_name: 'Sample relationships'
+#parent_description: 'Plots interrogating sample relationships, based on final count matrices'
 #plot_type: 'scatter'
 #anchor: 'deseq2_pca'
 #pconfig:
diff --git a/assets/methods_description_template.yml b/workflows/rnaseq/assets/multiqc/methods_description_template.yml
similarity index 100%
rename from assets/methods_description_template.yml
rename to workflows/rnaseq/assets/multiqc/methods_description_template.yml
diff --git a/assets/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
similarity index 51%
rename from assets/multiqc_config.yml
rename to workflows/rnaseq/assets/multiqc/multiqc_config.yml
index e738f4854..136e03f1c 100644
--- a/assets/multiqc_config.yml
+++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
@@ -1,15 +1,79 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.14.0" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.14.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.15.0" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.15.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
-  "nf-core-rnaseq-methods-description":
+  # Important checks and failures
+  sample-status:
+    order: 5004
+  fail_trimmed_samples-module:
+    order: 5003
+  fail_mapped_samples-module:
+    order: 5002
+  fail_strand_check-module:
+    order: 5001
+  # Preprocessing and pre-alignment QC
+  fastqc_raw:
+    order: 4004
+  cutadapt:
+    order: 4003
+  fastp:
+    order: 4003
+  fastqc_trimmed:
+    order: 4002
+  # Alignment
+  star:
+    order: 3000
+  hisat2:
+    order: 3000
+  # Post-alignment QC
+  samtools:
+    order: 3000
+  dupradar-module:
+    order: 3000
+  featurecounts_biotype:
+    order: 3000
+  picard:
+    order: 3000
+  preseq:
+    order: 3000
+  qualimap:
+    order: 3000
+  rseqc:
+    order: 3000
+  umitools:
+    order: 3000
+  # Quantification
+  rsem:
+    order: 2000
+  salmon:
+    order: 2000
+  kallisto:
+    order: 2000
+  # Post-quantification QC
+  sample-relationships:
+    order: 1006
+  star_salmon_deseq2_pca:
+    order: 1005
+  star_salmon_deseq2_clustering:
+    order: 1004
+  salmon_deseq2_pca:
+    order: 1003
+  salmon_deseq2_clustering:
+    order: 1002
+  star_rsem_deseq2_pca:
+    order: 1001
+  star_rsem_deseq2_clustering:
+    order: 1000
+  # Summaries
+  "nf-core-rnaseq-methods-description-module":
     order: -1000
-  software_versions:
+  "software_versions-module":
     order: -1001
-  "nf-core-rnaseq-summary":
+  "nf-core-rnaseq-summary-module":
     order: -1002
 
 export_plots: true
 disable_version_detection: true
+sample_names_replace_exact: true
 
 # Run only these modules
 run_modules:
@@ -21,6 +85,7 @@ run_modules:
   - star
   - hisat2
   - rsem
+  - umitools
   - salmon
   - kallisto
   - samtools
@@ -30,36 +95,28 @@ run_modules:
   - qualimap
 
 # Order of modules
-top_modules:
-  - "fail_trimmed_samples"
-  - "fail_mapped_samples"
-  - "fail_strand_check"
-  - "star_rsem_deseq2_pca"
-  - "star_rsem_deseq2_clustering"
-  - "star_salmon_deseq2_pca"
-  - "star_salmon_deseq2_clustering"
-  - "salmon_deseq2_pca"
-  - "salmon_deseq2_clustering"
-  - "biotype_counts"
-  - "dupradar"
 
 module_order:
   - fastqc:
+      anchor: "fastqc_raw"
       name: "FastQC (raw)"
       info: "This section of the report shows FastQC results before adapter trimming."
       path_filters:
-        - "./fastqc/raw/*.zip"
+        - "*_raw*fastqc.zip"
   - cutadapt
   - fastp
   - fastqc:
+      anchor: "fastqc_trimmed"
       name: "FastQC (trimmed)"
       info: "This section of the report shows FastQC results after adapter trimming."
       path_filters:
-        - "./fastqc/trim/*.zip"
+        - "*_trimmed*fastqc.zip"
 
 # Don't show % Dups in the General Stats table (we have this from Picard)
 table_columns_visible:
-  fastqc:
+  "FastQC (raw)":
+    percent_duplicates: False
+  "FastQC (trimmed)":
     percent_duplicates: False
 
 extra_fn_clean_exts:
@@ -155,24 +212,56 @@ custom_data:
     plot_type: "table"
     pconfig:
       id: "fail_trimmed_samples_table"
-      table_title: "Samples failed trimming threshold"
+      title: "Samples failed trimming threshold"
       namespace: "Samples failed trimming threshold"
-      format: "{:.0f}"
   fail_mapped_samples:
     section_name: "WARNING: Fail Alignment Check"
     description: "List of samples that failed the STAR minimum mapped reads threshold specified via the '--min_mapped_reads' parameter, and hence were ignored for the downstream processing steps."
     plot_type: "table"
     pconfig:
       id: "fail_mapped_samples_table"
-      table_title: "Samples failed mapping threshold"
+      title: "Samples failed mapping threshold"
       namespace: "Samples failed mapping threshold"
-      format: "{:.2f}"
   fail_strand_check:
-    section_name: "WARNING: Fail Strand Check"
-    description: "List of samples that failed the strandedness check between that provided in the samplesheet and calculated by the <a href='http://rseqc.sourceforge.net/#infer-experiment-py'>RSeQC infer_experiment.py</a> tool."
+    section_name: "Strandedness Checks"
+    description: "<p>The strandedness used for analysis in this workflow can either be provided by the user or automatically inferred by <b>Salmon</b> using a sample of reads. In both cases, strandedness is verified at the end of the workflow using <b>RSeQC</b>'s <a href='http://rseqc.sourceforge.net/#infer-experiment-py'>infer_experiment.py</a> on genomic alignments. In this table, a pass indicates a match between the supplied strandedness (or that inferred by Salmon) and RSeQC results. A fail indicates a mismatch or 'undetermined' strandedness. 'Undetermined' strandedness can signal QC issues, including potential genomic DNA contamination.</p><p><b>Note:</b> Rows are duplicated for an 'auto' setting to allow comparison of statistics between inference methods.</p>"
     plot_type: "table"
     pconfig:
       id: "fail_strand_check_table"
-      table_title: "Samples failed strandedness check"
-      namespace: "Samples failed strandedness check"
-      format: "{:.2f}"
+      title: "Samples strandedness check"
+      namespace: "Samples strandedness check"
+    headers:
+      Status:
+        description: Pass if the strandedness inferred by RSeQC matches that provided by the user or predicted by Salmon. Fail otherwise.
+      Strand inference method:
+        description: Tool used to detect strandedness
+      Provided strandedness:
+        description: User-provided strandedness
+        cond_formatting_rules:
+          blue:
+            - s_eq: "auto"
+          black:
+            - s_eq: "forward"
+          grey:
+            - s_eq: "reverse"
+        cond_formatting_colours:
+          - grey: "#AAB7B8"
+          - black: "#17202A"
+      Inferred strandedness:
+        description: Interred strandedness
+        cond_formatting_rules:
+          blue:
+            - s_eq: "auto"
+          black:
+            - s_eq: "forward"
+          grey:
+            - s_eq: "reverse"
+        cond_formatting_colours:
+          - grey: "#AAB7B8"
+          - black: "#17202A"
+      Sense (%):
+        max: 100
+      Antisense (%):
+        max: 100
+      Unstranded (%):
+        max: 100
diff --git a/workflows/rnaseq/assets/multiqc/sample_status_header.txt b/workflows/rnaseq/assets/multiqc/sample_status_header.txt
new file mode 100644
index 000000000..0a76ff8b9
--- /dev/null
+++ b/workflows/rnaseq/assets/multiqc/sample_status_header.txt
@@ -0,0 +1,3 @@
+#parent_id: 'sample-status'
+#parent_name: 'Sample status checks'
+#parent_description: 'Reports on sample strandedness status, and any failures in trimming or mapping'
diff --git a/assets/rrna-db-defaults.txt b/workflows/rnaseq/assets/rrna-db-defaults.txt
similarity index 100%
rename from assets/rrna-db-defaults.txt
rename to workflows/rnaseq/assets/rrna-db-defaults.txt
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
new file mode 100755
index 000000000..0b702e641
--- /dev/null
+++ b/workflows/rnaseq/main.nf
@@ -0,0 +1,796 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT LOCAL MODULES/SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// MODULE: Loaded from modules/local/
+//
+include { DESEQ2_QC as DESEQ2_QC_STAR_SALMON } from '../../modules/local/deseq2_qc'
+include { DESEQ2_QC as DESEQ2_QC_RSEM        } from '../../modules/local/deseq2_qc'
+include { DESEQ2_QC as DESEQ2_QC_PSEUDO      } from '../../modules/local/deseq2_qc'
+include { MULTIQC_CUSTOM_BIOTYPE             } from '../../modules/local/multiqc_custom_biotype'
+
+//
+// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
+//
+include { ALIGN_STAR    } from '../../subworkflows/local/align_star'
+include { QUANTIFY_RSEM } from '../../subworkflows/local/quantify_rsem'
+include { checkSamplesAfterGrouping      } from '../../subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { multiqcTsvFromList             } from '../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness'
+include { getStarPercentMapped           } from '../../subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { biotypeInGtf                   } from '../../subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { getInferexperimentStrandedness } from '../../subworkflows/local/utils_nfcore_rnaseq_pipeline'
+include { methodsDescriptionText         } from '../../subworkflows/local/utils_nfcore_rnaseq_pipeline'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// MODULE: Installed directly from nf-core/modules
+//
+include { DUPRADAR                } from '../../modules/nf-core/dupradar'
+include { SAMTOOLS_SORT           } from '../../modules/nf-core/samtools/sort'
+include { PRESEQ_LCEXTRAP         } from '../../modules/nf-core/preseq/lcextrap'
+include { QUALIMAP_RNASEQ         } from '../../modules/nf-core/qualimap/rnaseq'
+include { STRINGTIE_STRINGTIE     } from '../../modules/nf-core/stringtie/stringtie'
+include { SUBREAD_FEATURECOUNTS   } from '../../modules/nf-core/subread/featurecounts'
+include { MULTIQC                 } from '../../modules/nf-core/multiqc'
+include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../../modules/nf-core/umitools/prepareforrsem'
+include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_FW          } from '../../modules/nf-core/bedtools/genomecov'
+include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_REV         } from '../../modules/nf-core/bedtools/genomecov'
+
+//
+// SUBWORKFLOW: Consisting entirely of nf-core/modules
+//
+include { paramsSummaryMap                 } from 'plugin/nf-validation'
+include { fromSamplesheet                  } from 'plugin/nf-validation'
+include { paramsSummaryMultiqc             } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML           } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { FASTQ_ALIGN_HISAT2               } from '../../subworkflows/nf-core/fastq_align_hisat2'
+include { BAM_SORT_STATS_SAMTOOLS          } from '../../subworkflows/nf-core/bam_sort_stats_samtools'
+include { BAM_MARKDUPLICATES_PICARD        } from '../../subworkflows/nf-core/bam_markduplicates_picard'
+include { BAM_RSEQC                        } from '../../subworkflows/nf-core/bam_rseqc'
+include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME        } from '../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools'
+include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME } from '../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools'
+include { BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG as BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD } from '../../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig'
+include { BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG as BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE } from '../../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig'
+include { QUANTIFY_PSEUDO_ALIGNMENT as QUANTIFY_STAR_SALMON } from '../../subworkflows/nf-core/quantify_pseudo_alignment'
+include { QUANTIFY_PSEUDO_ALIGNMENT                         } from '../../subworkflows/nf-core/quantify_pseudo_alignment'
+include { FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS              } from '../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    RUN MAIN WORKFLOW
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+// Header files for MultiQC
+ch_pca_header_multiqc           = file("$projectDir/workflows/rnaseq/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true)
+sample_status_header_multiqc    = file("$projectDir/workflows/rnaseq/assets/multiqc/sample_status_header.txt", checkIfExists: true)
+ch_clustering_header_multiqc    = file("$projectDir/workflows/rnaseq/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true)
+ch_biotypes_header_multiqc      = file("$projectDir/workflows/rnaseq/assets/multiqc/biotypes_header.txt", checkIfExists: true)
+ch_dummy_file                   = ch_pca_header_multiqc
+
+workflow RNASEQ {
+
+    take:
+    ch_samplesheet       // channel: path(sample_sheet.csv)
+    ch_versions          // channel: [ path(versions.yml) ]
+    ch_fasta             // channel: path(genome.fasta)
+    ch_gtf               // channel: path(genome.gtf)
+    ch_fai               // channel: path(genome.fai)
+    ch_chrom_sizes       // channel: path(genome.sizes)
+    ch_gene_bed          // channel: path(gene.bed)
+    ch_transcript_fasta  // channel: path(transcript.fasta)
+    ch_star_index        // channel: path(star/index/)
+    ch_rsem_index        // channel: path(rsem/index/)
+    ch_hisat2_index      // channel: path(hisat2/index/)
+    ch_salmon_index      // channel: path(salmon/index/)
+    ch_kallisto_index    // channel: [ meta, path(kallisto/index/) ]
+    ch_bbsplit_index     // channel: path(bbsplit/index/)
+    ch_ribo_db           // channel: path(sortmerna_fasta_list)
+    ch_sortmerna_index   // channel: path(sortmerna/index/)
+    ch_splicesites       // channel: path(genome.splicesites.txt)
+    make_sortmerna_index // boolean: Whether to create an index before running sortmerna
+
+    main:
+
+    ch_multiqc_files = Channel.empty()
+    ch_trim_status = Channel.empty()
+    ch_map_status = Channel.empty()
+    ch_strand_status = Channel.empty()
+
+    //
+    // Create channel from input file provided through params.input
+    //
+    Channel
+        .fromSamplesheet("input")
+        .map {
+            meta, fastq_1, fastq_2 ->
+                if (!fastq_2) {
+                    return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
+                } else {
+                    return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
+                }
+        }
+        .groupTuple()
+        .map {
+            checkSamplesAfterGrouping(it)
+        }
+        .set{ ch_fastq }
+
+    //
+    // Run RNA-seq FASTQ preprocessing subworkflow
+    //
+
+    // The subworkflow only has to do Salmon indexing if it discovers 'auto'
+    // samples, and if we haven't already made one elsewhere
+    salmon_index_available = params.salmon_index || (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon')
+
+    FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS (
+        ch_fastq,
+        ch_fasta,
+        ch_transcript_fasta,
+        ch_gtf,
+        ch_salmon_index,
+        ch_sortmerna_index,
+        ch_bbsplit_index,
+        ch_ribo_db,
+        params.skip_bbsplit,
+        params.skip_fastqc || params.skip_qc,
+        params.skip_trimming,
+        params.skip_umi_extract,
+        !salmon_index_available,
+        !params.sortmerna_index && params.remove_ribo_rna,
+        params.trimmer,
+        params.min_trimmed_reads,
+        params.save_trimmed,
+        params.remove_ribo_rna,
+        params.with_umi,
+        params.umi_discard_read,
+        params.stranded_threshold,
+        params.unstranded_threshold
+    )
+
+    ch_multiqc_files                  = ch_multiqc_files.mix(FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS.out.multiqc_files)
+    ch_versions                       = ch_versions.mix(FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS.out.versions)
+    ch_strand_inferred_filtered_fastq = FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS.out.reads
+    ch_trim_read_count                = FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS.out.trim_read_count
+
+    ch_trim_status = ch_trim_read_count
+        .map {
+            meta, num_reads ->
+                return [ meta.id, num_reads > params.min_trimmed_reads.toFloat() ]
+        }
+    //
+    // Get list of samples that failed trimming threshold for MultiQC report
+    //
+    ch_trim_read_count
+        .map {
+            meta, num_reads ->
+                if (num_reads <= params.min_trimmed_reads.toFloat()) {
+                    return [ "$meta.id\t$num_reads" ]
+                }
+        }
+        .collect()
+        .map {
+            tsv_data ->
+                def header = ["Sample", "Reads after trimming"]
+                sample_status_header_multiqc.text + multiqcTsvFromList(tsv_data, header)
+        }
+        .set { ch_fail_trimming_multiqc }
+
+    ch_multiqc_files = ch_multiqc_files.mix(ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv'))
+
+    //
+    // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with Salmon
+    //
+    ch_genome_bam       = Channel.empty()
+    ch_genome_bam_index = Channel.empty()
+    ch_star_log         = Channel.empty()
+    if (!params.skip_alignment && params.aligner == 'star_salmon') {
+        // Check if an AWS iGenome has been provided to use the appropriate version of STAR
+        def is_aws_igenome = false
+        if (params.fasta && params.gtf) {
+            if ((file(params.fasta).getName() - '.gz' == 'genome.fa') && (file(params.gtf).getName() - '.gz' == 'genes.gtf')) {
+                is_aws_igenome = true
+            }
+        }
+
+        ALIGN_STAR (
+            ch_strand_inferred_filtered_fastq,
+            ch_star_index.map { [ [:], it ] },
+            ch_gtf.map { [ [:], it ] },
+            params.star_ignore_sjdbgtf,
+            '',
+            params.seq_center ?: '',
+            is_aws_igenome,
+            ch_fasta.map { [ [:], it ] }
+        )
+        ch_genome_bam        = ALIGN_STAR.out.bam
+        ch_genome_bam_index  = ALIGN_STAR.out.bai
+        ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript
+        ch_star_log          = ALIGN_STAR.out.log_final
+        ch_multiqc_files = ch_multiqc_files.mix(ALIGN_STAR.out.stats.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(ALIGN_STAR.out.flagstat.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(ALIGN_STAR.out.idxstats.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(ch_star_log.collect{it[1]})
+
+        if (params.bam_csi_index) {
+            ch_genome_bam_index = ALIGN_STAR.out.csi
+        }
+        ch_versions = ch_versions.mix(ALIGN_STAR.out.versions)
+
+        //
+        // SUBWORKFLOW: Remove duplicate reads from BAM file based on UMIs
+        //
+        if (params.with_umi) {
+            // Deduplicate genome BAM file before downstream analysis
+            BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME (
+                ch_genome_bam.join(ch_genome_bam_index, by: [0]),
+                params.umitools_dedup_stats
+            )
+            ch_genome_bam       = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bam
+            ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bai
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.deduplog.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.stats.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.flagstat.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.idxstats.collect{it[1]})
+
+            if (params.bam_csi_index) {
+                ch_genome_bam_index  = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.csi
+            }
+            ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.versions)
+
+            // Co-ordinate sort, index and run stats on transcriptome BAM
+            BAM_SORT_STATS_SAMTOOLS (
+                ch_transcriptome_bam,
+                ch_transcript_fasta.map { [ [:], it ] }
+            )
+            ch_transcriptome_sorted_bam = BAM_SORT_STATS_SAMTOOLS.out.bam
+            ch_transcriptome_sorted_bai = BAM_SORT_STATS_SAMTOOLS.out.bai
+
+            // Deduplicate transcriptome BAM file before read counting with Salmon
+            BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME (
+                ch_transcriptome_sorted_bam.join(ch_transcriptome_sorted_bai, by: [0]),
+                params.umitools_dedup_stats
+            )
+
+            // Name sort BAM before passing to Salmon
+            SAMTOOLS_SORT (
+                BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bam,
+                ch_fasta.map { [ [:], it ] }
+            )
+
+            // Only run prepare_for_rsem.py on paired-end BAM files
+            SAMTOOLS_SORT
+                .out
+                .bam
+                .branch {
+                    meta, bam ->
+                        single_end: meta.single_end
+                            return [ meta, bam ]
+                        paired_end: !meta.single_end
+                            return [ meta, bam ]
+                }
+                .set { ch_umitools_dedup_bam }
+
+            // Fix paired-end reads in name sorted BAM file
+            // See: https://github.com/nf-core/rnaseq/issues/828
+            UMITOOLS_PREPAREFORSALMON (
+                ch_umitools_dedup_bam.paired_end.map { meta, bam -> [ meta, bam, [] ] }
+            )
+            ch_versions = ch_versions.mix(UMITOOLS_PREPAREFORSALMON.out.versions.first())
+
+            ch_umitools_dedup_bam
+                .single_end
+                .mix(UMITOOLS_PREPAREFORSALMON.out.bam)
+                .set { ch_transcriptome_bam }
+        }
+
+        //
+        // SUBWORKFLOW: Count reads from BAM alignments using Salmon
+        //
+        QUANTIFY_STAR_SALMON (
+            ch_samplesheet.map { [ [:], it ] },
+            ch_transcriptome_bam,
+            ch_dummy_file,
+            ch_transcript_fasta,
+            ch_gtf,
+            params.gtf_group_features,
+            params.gtf_extra_attributes,
+            'salmon',
+            true,
+            params.salmon_quant_libtype ?: '',
+            params.kallisto_quant_fraglen,
+            params.kallisto_quant_fraglen_sd
+        )
+        ch_versions = ch_versions.mix(QUANTIFY_STAR_SALMON.out.versions)
+
+        if (!params.skip_qc & !params.skip_deseq2_qc) {
+            DESEQ2_QC_STAR_SALMON (
+                QUANTIFY_STAR_SALMON.out.counts_gene_length_scaled.map { it[1] },
+                ch_pca_header_multiqc,
+                ch_clustering_header_multiqc
+            )
+            ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_STAR_SALMON.out.pca_multiqc.collect())
+            ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_STAR_SALMON.out.dists_multiqc.collect())
+            ch_versions = ch_versions.mix(DESEQ2_QC_STAR_SALMON.out.versions)
+        }
+    }
+
+    //
+    // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with RSEM
+    //
+    if (!params.skip_alignment && params.aligner == 'star_rsem') {
+        QUANTIFY_RSEM (
+            ch_strand_inferred_filtered_fastq,
+            ch_rsem_index,
+            ch_fasta.map { [ [:], it ] }
+        )
+        ch_genome_bam       = QUANTIFY_RSEM.out.bam
+        ch_genome_bam_index = QUANTIFY_RSEM.out.bai
+        ch_star_log         = QUANTIFY_RSEM.out.logs
+        ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_RSEM.out.stats.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_RSEM.out.flagstat.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_RSEM.out.idxstats.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(ch_star_log.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_RSEM.out.stat.collect{it[1]})
+
+        if (params.bam_csi_index) {
+            ch_genome_bam_index = QUANTIFY_RSEM.out.csi
+        }
+        ch_versions = ch_versions.mix(QUANTIFY_RSEM.out.versions)
+
+        if (!params.skip_qc & !params.skip_deseq2_qc) {
+            DESEQ2_QC_RSEM (
+                QUANTIFY_RSEM.out.merged_counts_gene,
+                ch_pca_header_multiqc,
+                ch_clustering_header_multiqc
+            )
+            ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_RSEM.out.pca_multiqc.collect())
+            ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_RSEM.out.dists_multiqc.collect())
+            ch_versions = ch_versions.mix(DESEQ2_QC_RSEM.out.versions)
+        }
+    }
+
+    //
+    // SUBWORKFLOW: Alignment with HISAT2
+    //
+    if (!params.skip_alignment && params.aligner == 'hisat2') {
+        FASTQ_ALIGN_HISAT2 (
+            ch_strand_inferred_filtered_fastq,
+            ch_hisat2_index.map { [ [:], it ] },
+            ch_splicesites.map { [ [:], it ] },
+            ch_fasta.map { [ [:], it ] }
+        )
+        ch_genome_bam       = FASTQ_ALIGN_HISAT2.out.bam
+        ch_genome_bam_index = FASTQ_ALIGN_HISAT2.out.bai
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.stats.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.flagstat.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.idxstats.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.summary.collect{it[1]})
+
+        if (params.bam_csi_index) {
+            ch_genome_bam_index = FASTQ_ALIGN_HISAT2.out.csi
+        }
+        ch_versions = ch_versions.mix(FASTQ_ALIGN_HISAT2.out.versions)
+
+        //
+        // SUBWORKFLOW: Remove duplicate reads from BAM file based on UMIs
+        //
+        if (params.with_umi) {
+            BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME (
+                ch_genome_bam.join(ch_genome_bam_index, by: [0]),
+                params.umitools_dedup_stats
+            )
+            ch_genome_bam       = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bam
+            ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bai
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.deduplog.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.stats.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.flagstat.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.idxstats.collect{it[1]})
+            if (params.bam_csi_index) {
+                ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.csi
+            }
+            ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.versions)
+        }
+    }
+
+    //
+    // Filter channels to get samples that passed STAR minimum mapping percentage
+    //
+    if (!params.skip_alignment && params.aligner.contains('star')) {
+        ch_star_log
+            .map { meta, align_log -> [ meta ] + getStarPercentMapped(params, align_log) }
+            .set { ch_percent_mapped }
+
+        // Save status for workflow summary
+        ch_map_status = ch_percent_mapped
+            .map {
+                meta, mapped, pass ->
+                    return [ meta.id, pass ]
+            }
+
+        ch_genome_bam
+            .join(ch_percent_mapped, by: [0])
+            .map { meta, ofile, mapped, pass -> if (pass) [ meta, ofile ] }
+            .set { ch_genome_bam }
+
+        ch_genome_bam_index
+            .join(ch_percent_mapped, by: [0])
+            .map { meta, ofile, mapped, pass -> if (pass) [ meta, ofile ] }
+            .set { ch_genome_bam_index }
+
+        ch_percent_mapped
+            .branch { meta, mapped, pass ->
+                pass: pass
+                    return [ "$meta.id\t$mapped" ]
+                fail: !pass
+                    return [ "$meta.id\t$mapped" ]
+            }
+            .set { ch_pass_fail_mapped }
+
+        ch_pass_fail_mapped
+            .fail
+            .collect()
+            .map {
+                tsv_data ->
+                    def header = ["Sample", "STAR uniquely mapped reads (%)"]
+                    sample_status_header_multiqc.text + multiqcTsvFromList(tsv_data, header)
+            }
+            .set { ch_fail_mapping_multiqc }
+        ch_multiqc_files = ch_multiqc_files.mix(ch_fail_mapping_multiqc.collectFile(name: 'fail_mapped_samples_mqc.tsv'))
+    }
+
+    //
+    // MODULE: Run Preseq
+    //
+    if (!params.skip_alignment && !params.skip_qc && !params.skip_preseq) {
+        PRESEQ_LCEXTRAP (
+            ch_genome_bam
+        )
+        ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_LCEXTRAP.out.lc_extrap.collect{it[1]})
+        ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first())
+    }
+
+    //
+    // SUBWORKFLOW: Mark duplicate reads
+    //
+    if (!params.skip_alignment && !params.skip_markduplicates && !params.with_umi) {
+        BAM_MARKDUPLICATES_PICARD (
+            ch_genome_bam,
+            ch_fasta.map { [ [:], it ] },
+            ch_fai.map { [ [:], it ] }
+        )
+        ch_genome_bam       = BAM_MARKDUPLICATES_PICARD.out.bam
+        ch_genome_bam_index = BAM_MARKDUPLICATES_PICARD.out.bai
+        ch_multiqc_files = ch_multiqc_files.mix(BAM_MARKDUPLICATES_PICARD.out.stats.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(BAM_MARKDUPLICATES_PICARD.out.flagstat.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(BAM_MARKDUPLICATES_PICARD.out.idxstats.collect{it[1]})
+        ch_multiqc_files = ch_multiqc_files.mix(BAM_MARKDUPLICATES_PICARD.out.metrics.collect{it[1]})
+
+        if (params.bam_csi_index) {
+            ch_genome_bam_index = BAM_MARKDUPLICATES_PICARD.out.csi
+        }
+        ch_versions = ch_versions.mix(BAM_MARKDUPLICATES_PICARD.out.versions)
+    }
+
+    //
+    // MODULE: STRINGTIE
+    //
+    if (!params.skip_alignment && !params.skip_stringtie) {
+        STRINGTIE_STRINGTIE (
+            ch_genome_bam,
+            ch_gtf
+        )
+        ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions.first())
+    }
+
+    //
+    // MODULE: Feature biotype QC using featureCounts
+    //
+    def biotype = params.gencode ? "gene_type" : params.featurecounts_group_type
+    if (!params.skip_alignment && !params.skip_qc && !params.skip_biotype_qc && biotype) {
+
+        ch_gtf
+            .map { biotypeInGtf(it, biotype) }
+            .set { biotype_in_gtf }
+
+        // Prevent any samples from running if GTF file doesn't have a valid biotype
+        ch_genome_bam
+            .combine(ch_gtf)
+            .combine(biotype_in_gtf)
+            .filter { it[-1] }
+            .map { it[0..<it.size()-1] }
+            .set { ch_featurecounts }
+
+        SUBREAD_FEATURECOUNTS (
+            ch_featurecounts
+        )
+        ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS.out.versions.first())
+
+        MULTIQC_CUSTOM_BIOTYPE (
+            SUBREAD_FEATURECOUNTS.out.counts,
+            ch_biotypes_header_multiqc
+        )
+        ch_multiqc_files = ch_multiqc_files.mix(MULTIQC_CUSTOM_BIOTYPE.out.tsv.collect{it[1]})
+        ch_versions = ch_versions.mix(MULTIQC_CUSTOM_BIOTYPE.out.versions.first())
+    }
+
+    //
+    // MODULE: Genome-wide coverage with BEDTools
+    //
+    if (!params.skip_alignment && !params.skip_bigwig) {
+
+        ch_genomecov_input = ch_genome_bam.map { meta, bam -> [ meta, bam, 1 ] }
+
+        BEDTOOLS_GENOMECOV_FW (
+            ch_genomecov_input,
+            [],
+            'bedGraph',
+            true
+        )
+        BEDTOOLS_GENOMECOV_REV (
+            ch_genomecov_input,
+            [],
+            'bedGraph',
+            true
+        )
+
+        ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV_FW.out.versions.first())
+
+        //
+        // SUBWORKFLOW: Convert bedGraph to bigWig
+        //
+        BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD (
+            BEDTOOLS_GENOMECOV_FW.out.genomecov,
+            ch_chrom_sizes
+        )
+        ch_versions = ch_versions.mix(BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD.out.versions)
+
+        BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE (
+            BEDTOOLS_GENOMECOV_REV.out.genomecov,
+            ch_chrom_sizes
+        )
+    }
+
+    //
+    // MODULE: Downstream QC steps
+    //
+    if (!params.skip_alignment && !params.skip_qc) {
+        if (!params.skip_qualimap) {
+            QUALIMAP_RNASEQ (
+                ch_genome_bam,
+                ch_gtf.map { [ [:], it ] }
+            )
+            ch_multiqc_files = ch_multiqc_files.mix(QUALIMAP_RNASEQ.out.results.collect{it[1]})
+            ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions.first())
+        }
+
+        if (!params.skip_dupradar) {
+            DUPRADAR (
+                ch_genome_bam,
+                ch_gtf.map { [ [:], it ] }
+            )
+            ch_multiqc_files = ch_multiqc_files.mix(DUPRADAR.out.multiqc.collect{it[1]})
+            ch_versions = ch_versions.mix(DUPRADAR.out.versions.first())
+        }
+
+        // Get RSeqC modules to run
+        def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
+        if (params.bam_csi_index) {
+            for (rseqc_module in ['read_distribution', 'inner_distance', 'tin']) {
+                if (rseqc_modules.contains(rseqc_module)) {
+                    rseqc_modules.remove(rseqc_module)
+                }
+            }
+        }
+        if (!params.skip_rseqc && rseqc_modules.size() > 0) {
+            BAM_RSEQC (
+                ch_genome_bam.join(ch_genome_bam_index, by: [0]),
+                ch_gene_bed,
+                rseqc_modules
+            )
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_RSEQC.out.bamstat_txt.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_RSEQC.out.inferexperiment_txt.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_RSEQC.out.innerdistance_freq.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_RSEQC.out.junctionannotation_log.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_RSEQC.out.junctionsaturation_rscript.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_RSEQC.out.readdistribution_txt.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_RSEQC.out.readduplication_pos_xls.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(BAM_RSEQC.out.tin_txt.collect{it[1]})
+            ch_versions = ch_versions.mix(BAM_RSEQC.out.versions)
+
+            // Compare predicted supplied or Salmon-predicted strand with what we get from RSeQC
+            ch_strand_comparison = BAM_RSEQC.out.inferexperiment_txt
+                .map {
+                    meta, strand_log ->
+                        def rseqc_inferred_strand = getInferexperimentStrandedness(strand_log, stranded_threshold = params.stranded_threshold, unstranded_threshold = params.unstranded_threshold)
+                        rseqc_strandedness = rseqc_inferred_strand.inferred_strandedness
+
+                        def status = 'fail'
+                        def multiqc_lines = []
+                        if (meta.salmon_strand_analysis) {
+                            salmon_strandedness = meta.salmon_strand_analysis.inferred_strandedness
+
+                            if (salmon_strandedness == rseqc_strandedness && rseqc_strandedness != 'undetermined') {
+                                status = 'pass'
+                            }
+                            multiqc_lines = [
+                                "$meta.id \tSalmon\t$status\tauto\t${meta.salmon_strand_analysis.values().join('\t')}",
+                                "$meta.id\tRSeQC\t$status\tauto\t${rseqc_inferred_strand.values().join('\t')}"
+                            ]
+                        }
+                        else {
+                            if (meta.strandedness == rseqc_strandedness) {
+                                status = 'pass'
+                            }
+                            multiqc_lines = [ "$meta.id\tRSeQC\t$status\t$meta.strandedness\t${rseqc_inferred_strand.values().join('\t')}" ]
+                        }
+                        return [ meta, status, multiqc_lines ]
+                }
+                .multiMap {
+                    meta, status, multiqc_lines ->
+                        status: [ meta.id, status == 'pass' ]
+                        multiqc_lines: multiqc_lines
+                }
+
+            // Store the statuses for output
+            ch_strand_status = ch_strand_comparison.status
+
+            // Take the lines formatted for MultiQC and output
+            ch_strand_comparison.multiqc_lines
+                .flatten()
+                .collect()
+                .map {
+                    tsv_data ->
+                        def header = [
+                            "Sample",
+                            "Strand inference method",
+                            "Status",
+                            "Provided strandedness",
+                            "Inferred strandedness",
+                            "Sense (%)",
+                            "Antisense (%)",
+                            "Unstranded (%)"
+                        ]
+                        sample_status_header_multiqc.text + multiqcTsvFromList(tsv_data, header)
+                }
+                .set { ch_fail_strand_multiqc }
+
+            ch_multiqc_files = ch_multiqc_files.mix(ch_fail_strand_multiqc.collectFile(name: 'fail_strand_check_mqc.tsv'))
+        }
+    }
+
+    //
+    // SUBWORKFLOW: Pseudoalignment and quantification with Salmon
+    //
+    if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
+
+        if (params.pseudo_aligner == 'salmon') {
+            ch_pseudo_index = ch_salmon_index
+        } else {
+            ch_pseudo_index = ch_kallisto_index
+        }
+
+        QUANTIFY_PSEUDO_ALIGNMENT (
+            ch_samplesheet.map { [ [:], it ] },
+            ch_strand_inferred_filtered_fastq,
+            ch_pseudo_index,
+            ch_dummy_file,
+            ch_gtf,
+            params.gtf_group_features,
+            params.gtf_extra_attributes,
+            params.pseudo_aligner,
+            false,
+            params.salmon_quant_libtype ?: '',
+            params.kallisto_quant_fraglen,
+            params.kallisto_quant_fraglen_sd
+        )
+        ch_counts_gene_length_scaled = QUANTIFY_PSEUDO_ALIGNMENT.out.counts_gene_length_scaled
+        ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_PSEUDO_ALIGNMENT.out.multiqc.collect{it[1]})
+        ch_versions = ch_versions.mix(QUANTIFY_PSEUDO_ALIGNMENT.out.versions)
+
+        if (!params.skip_qc & !params.skip_deseq2_qc) {
+            DESEQ2_QC_PSEUDO (
+                ch_counts_gene_length_scaled.map { it[1] },
+                ch_pca_header_multiqc,
+                ch_clustering_header_multiqc
+            )
+            ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_PSEUDO.out.pca_multiqc.collect())
+            ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_PSEUDO.out.dists_multiqc.collect())
+            ch_versions = ch_versions.mix(DESEQ2_QC_PSEUDO.out.versions)
+        }
+    }
+
+    //
+    // Collate and save software versions
+    //
+    softwareVersionsToYAML(ch_versions)
+        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_rnaseq_software_mqc_versions.yml', sort: true, newLine: true)
+        .set { ch_collated_versions }
+
+    //
+    // MODULE: MultiQC
+    //
+    ch_multiqc_report = Channel.empty()
+
+    if (!params.skip_multiqc) {
+
+        // Load MultiQC configuration files
+        ch_multiqc_config        = Channel.fromPath("$projectDir/workflows/rnaseq/assets/multiqc/multiqc_config.yml", checkIfExists: true)
+        ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
+        ch_multiqc_logo          = params.multiqc_logo   ? Channel.fromPath(params.multiqc_logo)   : Channel.empty()
+
+        // Prepare the workflow summary
+        ch_workflow_summary = Channel.value(
+            paramsSummaryMultiqc(
+                paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+            )
+        ).collectFile(name: 'workflow_summary_mqc.yaml')
+
+        // Prepare the methods section
+        ch_methods_description = Channel.value(
+            methodsDescriptionText(
+                params.multiqc_methods_description
+                    ? file(params.multiqc_methods_description)
+                    : file("$projectDir/workflows/rnaseq/assets/multiqc/methods_description_template.yml", checkIfExists: true)
+            )
+        ).collectFile(name: 'methods_description_mqc.yaml')
+
+        // Add summary, versions, and methods to the MultiQC input file list
+        ch_multiqc_files = ch_multiqc_files
+            .mix(ch_workflow_summary)
+            .mix(ch_collated_versions)
+            .mix(ch_methods_description)
+
+        // Provide MultiQC with rename patterns to ensure it uses sample names
+        // for single-techrep samples not processed by CAT_FASTQ, and trims out
+        // _raw or _trimmed
+
+        ch_name_replacements = ch_fastq
+            .map{ meta, reads ->
+                def name1 = file(reads[0][0]).simpleName + "\t" + meta.id + '_1'
+                def fastqcnames = meta.id + "_raw\t" + meta.id + "\n" + meta.id + "_trimmed\t" + meta.id
+                if (reads[0][1] ){
+                    def name2 = file(reads[0][1]).simpleName + "\t" + meta.id + '_2'
+                    def fastqcnames1 = meta.id + "_raw_1\t" + meta.id + "_1\n" + meta.id + "_trimmed_1\t" + meta.id + "_1"
+                    def fastqcnames2 = meta.id + "_raw_2\t" + meta.id + "_2\n" + meta.id + "_trimmed_2\t" + meta.id + "_2"
+                    return [ name1, name2, fastqcnames1, fastqcnames2 ]
+                } else{
+                    return [ name1, fastqcnames ]
+                }
+            }
+            .flatten()
+            .collectFile(name: 'name_replacement.txt', newLine: true)
+
+        MULTIQC (
+            ch_multiqc_files.collect(),
+            ch_multiqc_config.toList(),
+            ch_multiqc_custom_config.toList(),
+            ch_multiqc_logo.toList(),
+            ch_name_replacements,
+            []
+        )
+        ch_multiqc_report = MULTIQC.out.report
+    }
+
+    emit:
+    trim_status    = ch_trim_status    // channel: [id, boolean]
+    map_status     = ch_map_status     // channel: [id, boolean]
+    strand_status  = ch_strand_status  // channel: [id, boolean]
+    multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
+    versions       = ch_versions       // channel: [ path(versions.yml) ]
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    THE END
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
diff --git a/workflows/rnaseq/nextflow.config b/workflows/rnaseq/nextflow.config
new file mode 100644
index 000000000..c7eeac733
--- /dev/null
+++ b/workflows/rnaseq/nextflow.config
@@ -0,0 +1,442 @@
+includeConfig "../../modules/local/multiqc_custom_biotype/nextflow.config"
+includeConfig "../../modules/nf-core/bbmap/bbsplit/nextflow.config"
+includeConfig "../../modules/nf-core/cat/fastq/nextflow.config"
+includeConfig "../../modules/nf-core/dupradar/nextflow.config"
+includeConfig "../../modules/nf-core/multiqc/nextflow.config"
+includeConfig "../../modules/nf-core/preseq/lcextrap/nextflow.config"
+includeConfig "../../modules/nf-core/qualimap/rnaseq/nextflow.config"
+includeConfig "../../modules/nf-core/sortmerna/nextflow.config"
+includeConfig "../../modules/nf-core/stringtie/stringtie/nextflow.config"
+includeConfig "../../modules/nf-core/subread/featurecounts/nextflow.config"
+includeConfig "../../subworkflows/local/align_star/nextflow.config"
+includeConfig "../../subworkflows/local/quantify_rsem/nextflow.config"
+includeConfig "../../subworkflows/nf-core/quantify_pseudo_alignment/nextflow.config"
+includeConfig "../../subworkflows/nf-core/bam_markduplicates_picard/nextflow.config"
+includeConfig "../../subworkflows/nf-core/bam_rseqc/nextflow.config"
+includeConfig "../../subworkflows/nf-core/fastq_align_hisat2/nextflow.config"
+includeConfig "../../subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config"
+includeConfig "../../subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config"
+includeConfig "../../subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config"
+
+//
+// STAR Salmon alignment options
+//
+
+if (!params.skip_alignment && params.aligner == 'star_salmon') {
+    process {
+        withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
+            ext.args   = { params.extra_salmon_quant_args ?: '' }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') || filename.endsWith('_format_counts.json') ? null : filename }
+            ]
+        }
+
+        withName: '.*:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE' {
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: '.*:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT' {
+            ext.prefix = { "${quant_type}.merged" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: '.*:QUANTIFY_STAR_SALMON:SE_.*' {
+            ext.prefix = { "${params.pseudo_aligner}.merged" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.log') ? null : filename }
+            ]
+        }
+        withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts" }
+        }
+        withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE_SCALED' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_scaled" }
+        }
+        withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_length_scaled" }
+        }
+        withName: '.*:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.transcript_counts" }
+        }
+    }
+
+    if (params.with_umi) {
+        process {
+            withName: 'NFCORE_RNASEQ:RNASEQ:SAMTOOLS_SORT' {
+                ext.args   = '-n'
+                ext.prefix = { "${meta.id}.umi_dedup.transcriptome" }
+                publishDir = [
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bam',
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
+                ]
+            }
+
+            withName: 'NFCORE_RNASEQ:RNASEQ:UMITOOLS_PREPAREFORSALMON' {
+                ext.prefix = { "${meta.id}.umi_dedup.transcriptome.filtered" }
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umitools/prepare_for_salmon_log" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log'
+                    ],
+                    [
+                        path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.bam',
+                        saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
+                    ]
+                ]
+            }
+
+            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
+                ext.prefix = { "${meta.id}.transcriptome.sorted" }
+                publishDir = [
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bam',
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
+                ]
+            }
+
+            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
+                publishDir = [
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bai',
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
+                ]
+            }
+
+            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
+                ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
+                publishDir = [
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}/samtools_stats" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.{stats,flagstat,idxstats}',
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
+                ext.args   = { [
+                    meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
+                    params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
+                    params.umitools_umi_separator   ? "--umi-separator='${params.umitools_umi_separator}'" : ''
+                ].join(' ').trim() }
+                ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umitools" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.tsv'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umitools/transcriptomic_dedup_log" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log'
+                    ],
+                    [
+                        path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.bam',
+                        saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
+                    ]
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
+                publishDir = [
+                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.bai',
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
+                ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.{stats,flagstat,idxstats}'
+                ]
+            }
+        }
+    }
+}
+
+//
+// General alignment options
+//
+
+if (!params.skip_alignment) {
+    process {
+        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
+            ext.prefix = { "${meta.id}.sorted.bam" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}/samtools_stats" },
+                mode: params.publish_dir_mode,
+                pattern: "*.{stats,flagstat,idxstats}"
+            ]
+        }
+
+        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
+            ext.prefix = { "${meta.id}.sorted" }
+            publishDir = [
+                path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
+                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
+                    ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
+                mode: params.publish_dir_mode,
+                pattern: "*.bam",
+                saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
+                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
+                    ) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
+            ]
+        }
+
+        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
+            ext.args   = { params.bam_csi_index ? '-c' : '' }
+            publishDir = [
+                path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
+                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
+                    ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
+                mode: params.publish_dir_mode,
+                pattern: "*.{bai,csi}",
+                saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
+                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
+                    ) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
+            ]
+        }
+    }
+
+    if (params.with_umi && ['star_salmon','hisat2'].contains(params.aligner)) {
+        process {
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
+                ext.args   = { [
+                    meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
+                    params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
+                    params.umitools_umi_separator   ? "--umi-separator='${params.umitools_umi_separator}'" : ''
+                ].join(' ').trim() }
+                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umitools" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.tsv'
+                    ],
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umitools/genomic_dedup_log" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log'
+                    ],
+                    [
+                        path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.bam',
+                        saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
+                    ]
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
+                ext.args   = { params.bam_csi_index ? '-c' : '' }
+                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
+                publishDir = [
+                    path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.{bai,csi}',
+                    saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
+                ext.prefix = { "${meta.id}.umi_dedup.sorted.bam" }
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.{stats,flagstat,idxstats}'
+                ]
+            }
+        }
+    }
+}
+
+//
+// bigWig coverage options
+//
+if (!params.skip_alignment && !params.skip_bigwig) {
+    process {
+        withName: 'BEDTOOLS_GENOMECOV_FW' {
+            ext.prefix = { meta.strandedness == 'reverse' ? meta.id + '.reverse' :  meta.id + '.forward' }
+            ext.args   = '-split -du -strand + -bg'
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: 'BEDTOOLS_GENOMECOV_REV' {
+            ext.prefix = { meta.strandedness == 'reverse' ? meta.id + '.forward' :  meta.id + '.reverse' }
+            ext.args   = '-split -du -strand - -bg'
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
+            ext.prefix = { "${meta.id}.clip.forward" }
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
+            ext.prefix = { "${meta.id}.forward" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}/bigwig" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP' {
+            ext.prefix = { "${meta.id}.clip.reverse" }
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
+            ext.prefix = { "${meta.id}.reverse" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}/bigwig" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+    }
+}
+
+//
+// DESeq2 QC options
+//
+
+if (!params.skip_alignment && params.aligner == 'star_salmon') {
+    if (!params.skip_qc & !params.skip_deseq2_qc) {
+        process {
+            withName: 'DESEQ2_QC_STAR_SALMON' {
+                ext.args   = { [
+                    "--id_col 1",
+                    "--sample_suffix ''",
+                    "--count_col 3",
+                    params.deseq2_vst ? '--vst TRUE' : ''
+                ].join(' ').trim() }
+                ext.args2  = 'star_salmon'
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
+                ]
+            }
+        }
+    }
+}
+
+if (!params.skip_alignment && params.aligner == 'star_rsem') {
+    if (!params.skip_qc & !params.skip_deseq2_qc) {
+        process {
+            withName: 'DESEQ2_QC_RSEM' {
+                ext.args   = { [
+                    "--id_col 1",
+                    "--sample_suffix ''",
+                    "--count_col 3",
+                    params.deseq2_vst ? '--vst TRUE' : ''
+                ].join(' ').trim() }
+                ext.args2  = 'star_rsem'
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
+                ]
+            }
+        }
+    }
+}
+
+//
+// Pseudo-alignment options
+//
+
+if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
+    process {
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE' {
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT' {
+            ext.prefix = { "${quant_type}.merged" }
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*' {
+            ext.args = '--assay_names counts,abundance'
+            publishDir = [
+                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.log') ? null : filename }
+            ]
+        }
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts" }
+        }
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_scaled" }
+        }
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_length_scaled" }
+        }
+        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT' {
+            ext.prefix = { "${params.pseudo_aligner}.merged.transcript_counts" }
+        }
+    }
+
+    if (!params.skip_qc & !params.skip_deseq2_qc) {
+        process {
+            withName: 'DESEQ2_QC_PSEUDO' {
+                ext.args   = { [
+                    "--id_col 1",
+                    "--sample_suffix ''",
+                    "--count_col 3",
+                    params.deseq2_vst ? '--vst TRUE' : ''
+                ].join(' ').trim() }
+                ext.args2  = { params.pseudo_aligner }
+                publishDir = [
+                    path: { "${params.outdir}/${params.pseudo_aligner}/deseq2_qc" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
+                ]
+            }
+        }
+    }
+}