Merge pull request nf-core#744 from nf-core/nf-core-template-merge-3.5.1

ramprasadn · web-flow · commit cdbf77d19235 · 2025-11-21T15:37:03.000+01:00
Important! Template update for nf-core/tools v3.5.1
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -39,7 +39,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -127,7 +127,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -84,7 +84,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -15,10 +15,9 @@ jobs:
           echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - name: get description
-        id: get_topics
+        id: get_description
         run: |
-          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT
-
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -27,9 +26,7 @@ jobs:
           # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            ${{ steps.get_topics.outputs.description }}
-
+            ${{ steps.get_description.outputs.description }}
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -8,7 +8,7 @@ lint:
     - docs/images/nf-core-raredisease_logo_light.png
     - assets/nf-core-raredisease_logo_light.png
   modules_config: false
-nf_core_version: 3.4.1
+nf_core_version: 3.5.1
 repository_type: pipeline
 template:
   author: Clinical Genomics Stockholm
diff --git a/.prettierignore b/.prettierignore
@@ -12,3 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/
diff --git a/README.md b/README.md
@@ -5,14 +5,14 @@
   </picture>
 </h1>
 
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/raredisease)
+[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)
 [![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 [![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/modules.json b/modules.json
@@ -310,7 +310,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
+                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
                         "installed_by": ["modules"]
                     },
                     "ngsbits/samplegender": {
@@ -549,7 +549,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
@@ -39,7 +39,7 @@ workflow PIPELINE_INITIALISATION {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
@@ -64,7 +64,7 @@ workflow PIPELINE_INITIALISATION {
 \033[0;35m  nf-core/raredisease ${workflow.manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
+    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> "    https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 
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
@@ -878,37 +878,57 @@ workflow RAREDISEASE {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-    softwareVersionsToYAML(ch_versions)
+    //
+    // Collate and save software versions
+    //
+    def topic_versions = Channel.topic("versions")
+        .distinct()
+        .branch { entry ->
+            versions_file: entry instanceof Path
+            versions_tuple: true
+        }
+
+    def topic_versions_string = topic_versions.versions_tuple
+        .map { process, tool, version ->
+            [ process[process.lastIndexOf(':')+1..-1], "  ${tool}: ${version}" ]
+        }
+        .groupTuple(by:0)
+        .map { process, tool_versions ->
+            tool_versions.unique().sort()
+            "${process}:\n${tool_versions.join('\n')}"
+        }
+
+    softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
+        .mix(topic_versions_string)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
             name: 'nf_core_'  +  'raredisease_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }
 
-
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = Channel.fromPath(
+    ch_multiqc_config        = channel.fromPath(
         "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
     ch_multiqc_custom_config = params.multiqc_config ?
-        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        channel.empty()
     ch_multiqc_logo          = params.multiqc_logo ?
         Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
         Channel.fromPath("$projectDir/docs/images/nf-core-raredisease_logo_light.png", checkIfExists: true)
 
 
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    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)
-    ch_methods_description                = Channel.value(
+    ch_methods_description                = channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)

Original file line number	Diff line number	Diff line change
`@@ -39,7 +39,7 @@ jobs:`
`39`	`39`	`}`
`40`	`40`	`profiles: test_full`
`41`	`41`
`42`		`- - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4`
	`42`	`+ - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5`
`43`	`43`	`with:`
`44`	`44`	`name: Seqera Platform debug log file`
`45`	`45`	`path: \|`
Original file line number	Diff line number	Diff line change
`@@ -25,7 +25,7 @@ jobs:`
`25`	`25`	`}`
`26`	`26`	`profiles: test`
`27`	`27`
`28`		`- - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4`
	`28`	`+ - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5`
`29`	`29`	`with:`
`30`	`30`	`name: Seqera Platform debug log file`
`31`	`31`	`path: \|`