Merge pull request #52 from nf-core/ci-interproscan

feat: Add interproscan_run param

Author: olgabot

.github/CONTRIBUTING.md

@@ -78,7 +78,7 @@ If you wish to contribute a new step, please use the following coding standards:
 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
-8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+8. If applicable, add a new test in the `tests` directory.
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 

.github/actions/nf-test/action.yml

@@ -69,6 +69,7 @@ runs:
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
       run: |
         nf-test test \
+          --tag=CI \
           --profile=+${{ inputs.profile }} \
           --tap=test.tap \
           --verbose \

.github/workflows/linting.yml

@@ -3,9 +3,6 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -17,9 +14,9 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -36,13 +33,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -74,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
         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@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.github/workflows/nf-test.yml

@@ -94,6 +94,7 @@ jobs:
         NXF_VER:
           # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
           - "24.10.2"
+          - "24.04.2" # Absolute mininmum pipeline test version
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

.prettierrc.yml

@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2

README.md

@@ -30,18 +30,14 @@
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
-1. Functional Annotation
-  1. ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.
-1. Run ([`seqkit stats`](https://bioinf.shenwei.me/seqkit/usage/#stats)) to summarize input protein fasta files
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
-
-![Protein annotator metromap. Protein fasta files are summarized with `seqkit stats`, then functionally annotated with InterProScan, DIAMOND-blastp, UniFire, and Kmerseek](assets/proteinannotator-metromap.excalidraw.png)
 
 1. Run ([`seqkit stats`](https://bioinf.shenwei.me/seqkit/usage/#stats)) to summarize input protein fasta files
-2. Functional Annotation
-  1. ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.
+2. Functional Annotation:
+   1. ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.
 3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
+![Protein annotator metromap. Protein fasta files are summarized with `seqkit stats`, then functionally annotated with InterProScan, DIAMOND-blastp, UniFire, and Kmerseek](assets/proteinannotator-metromap.excalidraw.png)
+
 ## Usage
 
 > [!NOTE]

conf/test.config

@@ -28,4 +28,5 @@ params {
     // From: https://github.com/nf-core/proteinfold/blob/1.1.1/conf/test.config
     // Example: https://github.com/nf-core/test-datasets/blob/proteinfold/testdata/samplesheet/v1.2/samplesheet.csv
     input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
+    run_interproscan = false
 }

conf/test_full.config

@@ -18,4 +18,5 @@ params {
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input = params.pipelines_testdata_base_path + 'proteinannotator/samplesheet/snap25-isoforms.csv'
+    run_interproscan = true
 }

modules.json

@@ -5,19 +5,19 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "mmseqs/search": {
+                    "interproscan": {
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
-                    "mtmalign/align": {
+                    "mmseqs/search": {
                         "branch": "master",
-                        "git_sha": "c7cfb9446fb3098e525089198ff232d795c20ef2",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
-                    "interproscan": {
+                    "mtmalign/align": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "c7cfb9446fb3098e525089198ff232d795c20ef2",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {