Merge pull request #630 from nf-core/nf-core-template-merge-3.0.2

Important! Template update for nf-core/tools v3.0.2
nf-core · Oct 14, 2024 · dbb3e8f · dbb3e8f
2 parents 3374172 + d3c51a6
commit dbb3e8f
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Showing 12 changed files with 88 additions and 53 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -11,14 +11,16 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
   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 }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/raredisease') }}"
     runs-on: ubuntu-latest
@@ -27,31 +29,40 @@ jobs:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
-        parameters:
-          - "-profile test"
-          - "-profile test_one_sample"
+        profile:
+          - "docker"
+          - "singularity"
+        test_name:
+          - "test"
+          - "test_one_sample"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - 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: "${{ 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)
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
         run: |
-          nextflow run ${GITHUB_WORKSPACE} ${{ matrix.parameters }},docker -stub --outdir ./results
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
-      - name: Run pipeline with test data (singularity)
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} ${{ matrix.parameters }},singularity -stub --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data (conda)
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} -stub --outdir ./results
diff --git a/.github/workflows/template_version_comment.yml b/.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).
           #
diff --git a/.gitignore b/.gitignore
@@ -6,4 +6,5 @@ results/
 testing/
 testing*
 *.pyc
+null/
 .prettierignore
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -9,7 +9,7 @@ lint:
     - docs/images/nf-core-raredisease_logo_light.png
     - assets/nf-core-raredisease_logo_light.png
   modules_config: false
-nf_core_version: 3.0.1
+nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
 template:

diff --git a/modules.json b/modules.json
@@ -294,7 +294,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "ngsbits/samplegender": {
@@ -518,12 +518,12 @@
                 "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"]
                     },
                     "utils_nfschema_plugin": {

diff --git a/modules/local/get_chrom_sizes.nf b/modules/local/get_chrom_sizes.nf
@@ -26,4 +26,15 @@ process GET_CHROM_SIZES {
         cut: \$(echo \$(cut --help 2>&1 | head -n 1 | cut -f1,2 -d' '))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${fai}.sizes
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cut: \$(echo \$(cut --help 2>&1 | head -n 1 | cut -f1,2 -d' '))
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/local/rename_align_files.nf b/modules/local/rename_align_files.nf
@@ -27,4 +27,14 @@ process RENAME_ALIGN_FILES {
         ln: \$(echo \$(ln --version 2>&1 | head -n 1 | cut -d ' ' -f4))
     END_VERSIONS
     """
+
+    stub:
+    """
+    ln -s $input ${meta.sample}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ln: \$(echo \$(ln --version 2>&1 | head -n 1 | cut -d ' ' -f4))
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
@@ -47,7 +47,6 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-
     //
     // Validate parameters and generate parameter summary to stdout
     //
@@ -57,13 +56,13 @@ workflow PIPELINE_INITIALISATION {
         null
     )
 
-
     //
     // Check config provided to the pipeline
     //
     UTILS_NFCORE_PIPELINE (
         nextflow_cli_args
     )
+
     //
     // Custom validation for pipeline parameters
     //
@@ -120,7 +119,6 @@ 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
-
     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

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -886,7 +886,6 @@ workflow RAREDISEASE {
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)