Merge branch 'dev' into improve_samplesheetToList

.github/workflows/ci.yml

@@ -12,6 +12,8 @@ env:
   NFT_VER: "0.9.0"
   NFT_WORKDIR: "~"
   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 }}"
@@ -40,7 +42,7 @@ jobs:
           echo ${{ steps.list.outputs.components }}
 
   test:
-    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})"
     needs: [nf-test-changes]
     if: needs.nf-test-changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
@@ -52,17 +54,51 @@ jobs:
           - "latest-everything"
         nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
         profile:
+          - "conda"
           - "docker"
-
+          - "singularity"
+        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: "${{ matrix.NXF_VER }}"
 
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          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: Set up Conda
+        if: matrix.profile == 'conda'
+        run: |
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
       - name: Install nf-test
         uses: nf-core/setup-nf-test@v1
         with:
@@ -78,6 +114,9 @@ jobs:
           python -m pip install --upgrade pip
           pip install pdiff
 
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Run nf-test
         run: |
           nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap

.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).
           #

.gitignore

@@ -10,3 +10,4 @@ test.xml
 testing*
 testing/
 work/
+null/

.nf-core.yml

@@ -12,7 +12,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest
-nf_core_version: 3.0.1
+nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
 template:

modules.json

@@ -104,7 +104,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
@@ -352,12 +352,12 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb",
+                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb",
+                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf

@@ -49,7 +49,6 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-
     //
     // Validate parameters and generate parameter summary to stdout
     //
@@ -59,7 +58,6 @@ workflow PIPELINE_INITIALISATION {
         null
     )
 
-
     //
     // Check config provided to the pipeline
     //
@@ -92,7 +90,6 @@ 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

tests/default.nf.test.snap

@@ -83,8 +83,7 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {

tests/featurecounts_group_type.nf.test.snap

@@ -83,8 +83,7 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {

tests/hisat2.nf.test.snap

@@ -84,8 +84,7 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
@@ -1312,4 +1311,4 @@
         },
         "timestamp": "2024-10-10T12:37:31.888584"
     }
-}
+}

tests/kallisto.nf.test.snap

@@ -322,8 +322,7 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {

tests/min_mapped_reads.nf.test.snap

@@ -1261,8 +1261,7 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {

tests/remove_ribo_rna.nf.test.snap

@@ -1475,8 +1475,7 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {

tests/salmon.nf.test.snap

@@ -395,8 +395,7 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
@@ -405,4 +404,4 @@
         },
         "timestamp": "2024-10-10T07:07:48.845197"
     }
-}
+}

tests/skip_qc.nf.test.snap

@@ -69,8 +69,7 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
@@ -790,4 +789,4 @@
         },
         "timestamp": "2024-10-10T11:16:41.081492"
     }
-}
+}

tests/star_rsem.nf.test.snap

@@ -1354,8 +1354,7 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {