Merge pull request #16 from JoseEspinosa/updates

Add stub and update test

.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/reportho then the best place to ask is on the nf-core Slack [#reportho](https://nfcore.slack.com/channels/reportho) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
+> [!NOTE]
+> If you need help using or modifying nf-core/reportho then the best place to ask is on the nf-core Slack [#reportho](https://nfcore.slack.com/channels/reportho) 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
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/repo
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/reportho/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/reportho _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/linting.yml

@@ -35,7 +35,7 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:

.vscode/settings.json

@@ -1,4 +1,4 @@
 {
     "editor.defaultFormatter": "esbenp.prettier-vscode",
-    "editor.formatOnSave": true,
+    "editor.formatOnSave": true
 }

conf/modules.config

@@ -46,7 +46,7 @@ process {
         ]
     }
 
-    withName: 'FETCH_INSPECTOR_GROUP_LOCAL|FETCH_INSPECTOR_GROUP_ONLINE' {
+    withName: 'FETCH_INSPECTOR_GROUP_ONLINE' {
         publishDir = [
             path: { "${params.outdir}/orthologs/orthoinspector" },
             mode: params.publish_dir_mode,

conf/test.config

@@ -29,3 +29,4 @@ params {
     skip_iqtree      = true
     fastme_bootstrap = 0
 }
+

modules.json

@@ -56,7 +56,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {

modules/local/convert_fasta.nf

@@ -28,4 +28,16 @@ process CONVERT_FASTA {
         Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fa
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }

modules/local/convert_phylip.nf

@@ -28,4 +28,16 @@ process CONVERT_PHYLIP {
         Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.phy
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }

modules/local/create_tcoffeetemplate.nf

@@ -20,7 +20,10 @@ process CREATE_TCOFFEETEMPLATE {
     prefix   = task.ext.prefix ?: "${meta.id}"
     """
     # Prep templates
-    for structure in \$(ls *.pdb); do id=`echo \$structure| awk  {'gsub(".pdb", "", \$0); print'}`; echo -e ">"\$id "_P_" "\${id}" >>${prefix}_template.txt ; done
+    for structure in \$(ls *.pdb); do
+        id=`echo \$structure | awk  {'gsub(".pdb", "", \$0); print'}`;
+        echo -e ">"\$id "_P_" "\${id}" >> ${prefix}_template.txt;
+    done
     """
 
     stub:

modules/local/dump_params.nf

@@ -8,6 +8,13 @@ process DUMP_PARAMS {
 
     input:
     tuple val(meta), path(exact)
+    val uniprot_query
+    val use_structures
+    val use_centroid
+    val min_score
+    val skip_downstream
+    val use_iqtree
+    val use_fastme
 
     output:
     tuple val(meta), path("params.yml"), emit: params
@@ -19,14 +26,19 @@ process DUMP_PARAMS {
     """
     cat <<- END_PARAMS > params.yml
     id: ${meta.id}
-    uniprot_query: ${params.uniprot_query}
+    uniprot_query: ${uniprot_query}
     exact_match: \$(cat $exact)
-    use_structures: ${params.use_structures}
-    use_centroid: ${params.use_centroid}
-    min_score: ${params.min_score}
-    skip_downstream: ${params.skip_downstream}
-    use_iqtree: ${params.use_iqtree}
-    use_fastme: ${params.use_fastme}
+    use_structures: ${use_structures}
+    use_centroid: ${use_centroid}
+    min_score: ${min_score}
+    skip_downstream: ${skip_downstream}
+    use_iqtree: ${use_iqtree}
+    use_fastme: ${use_fastme}
     END_PARAMS
     """
+
+    stub:
+    """
+    touch params.yml
+    """
 }

modules/local/fetch_afdb_structures.nf

@@ -31,4 +31,16 @@ process FETCH_AFDB_STRUCTURES {
         Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.phy
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}"
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }

modules/local/fetch_eggnog_group_local.nf

@@ -2,6 +2,11 @@ process FETCH_EGGNOG_GROUP_LOCAL {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
@@ -33,4 +38,15 @@ process FETCH_EGGNOG_GROUP_LOCAL {
     END_VERSIONS
     """
 
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_eggnog_group.txt
+    touch ${prefix}_eggnog_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }

modules/local/fetch_inspector_group_online.nf

@@ -32,4 +32,17 @@ process FETCH_INSPECTOR_GROUP_ONLINE {
         OrthoInspector Database: $inspector_version
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_inspector_group.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+        OrthoInspector Database: $inspector_version
+    END_VERSIONS
+    """
 }

modules/local/fetch_oma_group_local.nf

@@ -2,6 +2,11 @@ process FETCH_OMA_GROUP_LOCAL {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
@@ -36,4 +41,14 @@ process FETCH_OMA_GROUP_LOCAL {
     END_VERSIONS
     """
 
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_oma_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }

modules/local/fetch_oma_group_online.nf

@@ -33,4 +33,17 @@ process FETCH_OMA_GROUP_ONLINE {
     \$(get_oma_version.py)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_oma_group.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    \$(get_oma_version.py)
+    END_VERSIONS
+    """
 }

modules/local/fetch_panther_group_local.nf

@@ -7,6 +7,11 @@ process FETCH_PANTHER_GROUP_LOCAL {
         'https://depot.galaxyproject.org/singularity/python:3.10' :
         'biocontainers/python:3.10' }"
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     input:
     tuple val(meta), path(uniprot_id), path(taxid), path(exact)
     path panther_db
@@ -30,4 +35,15 @@ process FETCH_PANTHER_GROUP_LOCAL {
         Python: \$(python --version | cut -f2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_panther_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }

modules/local/fetch_panther_group_online.nf

@@ -32,4 +32,17 @@ process FETCH_PANTHER_GROUP_ONLINE {
         Panther Database: \$(cat panther_version.txt)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_panther_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+        Panther Database: \$(cat panther_version.txt)
+    END_VERSIONS
+    """
 }

modules/local/fetch_sequences_online.nf

@@ -33,4 +33,19 @@ process FETCH_SEQUENCES_ONLINE {
     \$(get_oma_version.py)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_orthologs.fa
+    touch ${prefix}_seq_hits.txt
+    touch ${prefix}_seq_misses.txt
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    \$(get_oma_version.py)
+    END_VERSIONS
+    """
 }

modules/local/filter_fasta.nf

@@ -2,6 +2,11 @@ process FILTER_FASTA {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
@@ -27,4 +32,15 @@ process FILTER_FASTA {
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_filtered.fa
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }

modules/local/filter_hits.nf

@@ -32,4 +32,17 @@ process FILTER_HITS {
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_minscore_000.txt
+    touch ${prefix}_centroid.txt
+    touch ${prefix}_filtered_hits.txt
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }