Merge pull request #3219 from nf-core/dev

Dev -> main for 3.0.2

.github/workflows/sync.yml

@@ -1,7 +1,7 @@
 name: Sync template
 on:
-  release:
-    types: [published]
+  # release:
+  #   types: [published]
   workflow_dispatch:
     inputs:
       testpipeline:
@@ -39,7 +39,7 @@ jobs:
         run: |
           if [ "${{ github.event.inputs.testpipeline }}" == "true" ]; then
             echo '{"pipeline":["testpipeline"]}' > pipeline_names.json
-          elif [ "${{ github.event.inputs.pipeline }}" != "all" ]; then
+          elif [ "${{ github.event.inputs.pipeline }}" != "all" ] && [ "${{ github.event.inputs.pipeline }}" != "" ]; then
             curl -O https://nf-co.re/pipeline_names.json
             # check if the pipeline exists
             if ! grep -q "\"${{ github.event.inputs.pipeline }}\"" pipeline_names.json; then

CHANGELOG.md

@@ -1,5 +1,23 @@
 # nf-core/tools: Changelog
 
+## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
+
+### Template
+
+- Add null/ to .gitignore ([#3191](https://github.com/nf-core/tools/pull/3191))
+- Parallelize pipeline GHA tests over docker/conda/singularity ([#3214](https://github.com/nf-core/tools/pull/3214))
+- Fix `template_version_comment.yml` github action ([#3212](https://github.com/nf-core/tools/pull/3212))
+- Fix pre-commit linting on pipeline template ([#3218](https://github.com/nf-core/tools/pull/3218))
+
+### Linting
+
+- Fix bug when linting schema params and when using `defaultIgnoreParams` ([#3213](https://github.com/nf-core/tools/pull/3213))
+
+### General
+
+- Use updated pipeline commands in docstrings ([#3215](https://github.com/nf-core/tools/pull/3215))
+- Disable automatic sync on release, fix handling empty pipeline input ([#3217](https://github.com/nf-core/tools/pull/3217))
+
 ## [v3.0.1 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.1) - [2024-10-09]
 
 ### Template

nf_core/pipeline-template/.github/workflows/ci.yml

@@ -1,5 +1,5 @@
 name: nf-core CI
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+# {% raw %}This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
   push:
     branches:
@@ -11,49 +11,75 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
-  group: "{% raw %}${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}{% endraw %}"
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "{% raw %}${{{% endraw %} github.event_name != 'push' || (github.event_name == 'push' && github.repository == '{{ name }}') {% raw %}}}{% endraw %}"
+    if: "${{{% endraw %} github.event_name != 'push' || (github.event_name == 'push' && github.repository == '{{ name }}') {% raw %}}}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        test_name:
+          - "test"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
+      - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
-          version: "{% raw %}${{ matrix.NXF_VER }}{% endraw %}"
+          version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
 
-      - name: Run pipeline with test data (docker)
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
 
-      - name: Run pipeline with test data (singularity)
-        # TODO nf-core: You can customise CI pipeline run tests as required
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
-        if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}"
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data (conda)
-        # TODO nf-core: You can customise CI pipeline run tests as required
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
-        if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}"
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results{% endraw %}

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -116,5 +116,4 @@ jobs:
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"
-          fi
-          {% endraw %}{% endif %}
+          fi{% endraw %}{% endif %}

nf_core/pipeline-template/.github/workflows/template_version_comment.yml

@@ -10,9 +10,11 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: nichmor/minimal-read-yaml@v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -24,20 +26,21 @@ jobs:
 
       - name: Check nf-core outdated
         id: nf_core_outdated
-        run: pip list --outdated | grep nf-core
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         if: |
-          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+          contains(env.OUTPUT, 'nf-core')
         with:
           repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
           allow-repeats: false
           message: |
-            ## :warning: Newer version of the nf-core template is available.
-
-            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
-            Please update your pipeline to the latest version.
-
-            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
           #{%- endraw %}

nf_core/pipeline-template/.gitignore

@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+null/

nf_core/pipeline-template/CITATIONS.md

@@ -15,12 +15,14 @@
 {% if fastqc %}- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
-> {% endif %}
+
+{%- endif %}
 
 {% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
-> {% endif %}
+
+{%- endif %}
 
 ## Software packaging/containerisation tools
 
@@ -43,4 +45,5 @@
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
 
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
-  > {%- endif %}
+
+  {%- endif %}

nf_core/pipeline-template/docs/output.md

@@ -64,7 +64,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 - `pipeline_info/`
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
     {%- if email %}
-  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %}
+  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.{% endif %}
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
   - Parameters used by the pipeline run: `params.json`.
 

nf_core/pipeline-template/main.nf

@@ -84,7 +84,8 @@ workflow {
         params.outdir,
         params.input
     )
-    {% endif %}
+    {%- endif %}
+
     //
     // WORKFLOW: Run main workflow
     //

nf_core/pipeline-template/modules.json

@@ -13,7 +13,7 @@
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}
@@ -23,12 +23,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
+                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
+                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {

nf_core/pipeline-template/nextflow.config

@@ -288,10 +288,10 @@ validation {
 """
         afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework
-  https://doi.org/10.1038/s41587-020-0439-x
+    https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+    https://github.com/${manifest.name}/blob/master/CITATIONS.md
 """{% endif %}
     }{% if is_nfcore %}
     summary {

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -51,7 +51,8 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-    {% if nf_schema %}
+    {%- if nf_schema %}
+
     //
     // Validate parameters and generate parameter summary to stdout
     //
@@ -60,7 +61,7 @@ workflow PIPELINE_INITIALISATION {
         validate_params,
         null
     )
-    {% endif %}
+    {%- endif %}
 
     //
     // Check config provided to the pipeline
@@ -70,6 +71,7 @@ workflow PIPELINE_INITIALISATION {
     )
 
     {%- if igenomes %}
+
     //
     // Custom validation for pipeline parameters
     //
@@ -123,7 +125,7 @@ workflow PIPELINE_COMPLETION {
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
-    {% endif %}
+    {%- endif %}
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     {% if adaptivecard or slackreport %}hook_url        //  string: hook URL for notifications{% endif %}