Merge remote-tracking branch 'origin/dev/cutadapt' into dev/cutadapt

.github/workflows/test.yaml

@@ -0,0 +1,105 @@
+name: Component Testing
+
+on:
+  pull_request:
+  push:
+    branches: [ '**' ]
+
+jobs:
+  run_ci_check_job:
+    runs-on: ubuntu-latest
+    outputs:
+      run_ci: ${{ steps.github_cli.outputs.check }}
+    steps:
+      - name: 'Check if branch has an existing pull request and the trigger was a push'
+        id: github_cli
+        run: |
+          pull_request=$(gh pr list -R ${{ github.repository }} -H ${{ github.ref_name }} --json url --state open --limit 1 | jq '.[0].url')
+          # If the branch has a PR and this run was triggered by a push event, do not run
+          if [[ "$pull_request" != "null" && "$GITHUB_REF_NAME" != "main" && "${{ github.event_name == 'push' }}" == "true" && "${{ !contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then
+            echo "check=false" >> $GITHUB_OUTPUT
+          else
+            echo "check=true" >> $GITHUB_OUTPUT
+          fi
+        env:
+           GH_TOKEN: ${{ github.token }}
+
+  # phase 1
+  list:
+    needs: run_ci_check_job
+    runs-on: ubuntu-latest
+    if: ${{ needs.run_ci_check_job.outputs.run_ci == 'true' }}
+
+    outputs:
+      matrix: ${{ steps.set_matrix.outputs.matrix }}
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Get head git commit message
+      id: get_head_commit_message
+      run: echo "HEAD_COMMIT_MESSAGE=$(git show -s --format=%s ${{ github.event.pull_request.head.sha || github.sha }})" >> "$GITHUB_OUTPUT"
+
+    - uses: viash-io/viash-actions/setup@v5
+
+    - name: Check if all config can be parsed if there is no unicode support
+      run: |
+        LANG=C viash ns list > /dev/null
+
+    - name: Get changed files
+      id: changed-files
+      uses: tj-actions/changed-files@v42
+      with:
+        separator: ";"
+        diff_relative: true
+
+    - id: ns_list
+      uses: viash-io/viash-actions/ns-list@v5
+      with:
+        platform: docker
+        format: json
+        query: ^(?!workflows)
+
+    - id: ns_list_filtered
+      uses: viash-io/viash-actions/project/detect-changed-components@v5
+      with:
+        input_file: "${{ steps.ns_list.outputs.output_file }}"
+
+    - id: set_matrix
+      run: |
+        echo "matrix=$(jq -c '[ .[] | 
+          { 
+            "name": (.functionality.namespace + "/" + .functionality.name),
+            "config": .info.config,
+            "dir": .info.config | capture("^(?<dir>.*\/)").dir
+          }
+        ]' ${{ contains(steps.get_head_commit_message.outputs.HEAD_COMMIT_MESSAGE, 'ci force') && steps.ns_list.outputs.output_file || steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT
+
+  # phase 2
+  viash_test:
+    needs: list
+    if: ${{ needs.list.outputs.matrix != '[]' && needs.list.outputs.matrix != '' }}
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        component: ${{ fromJson(needs.list.outputs.matrix) }}
+
+    steps:
+    # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.'
+    - uses: data-intuitive/reclaim-the-bytes@v2
+
+    - uses: actions/checkout@v4
+
+    - uses: viash-io/viash-actions/setup@v5
+
+    - name: Run test
+      timeout-minutes: 30
+      run: |
+        viash test \
+          "${{ matrix.component.config }}" \
+          --cpus 2 \
+          --memory "6gb"

.gitignore

@@ -0,0 +1,17 @@
+*.DS_Store
+*__pycache__
+
+# IDE ignores
+.idea/
+
+# R specific ignores
+.Rhistory
+.Rproj.user
+*.Rproj
+
+# viash specific ignores
+target/
+
+# nextflow specific ignores
+.nextflow*
+work

CHANGELOG.md

@@ -4,6 +4,10 @@
 
 ## NEW FEATURES
 
+* `arriba`: Detect gene fusions from RNA-seq data (PR #1).
+
+* `fastp`: An ultra-fast all-in-one FASTQ preprocessor (PR #3).
+
 ## MAJOR CHANGES
 
 ## MINOR CHANGES