Merge pull request #1628 from nf-core/nf-core-template-merge-3.5.1

pinin4fjords · web-flow · commit 1e56dca7421e · 2025-11-25T15:14:47.000Z
Important! Template update for nf-core/tools v3.5.1
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -44,7 +44,7 @@ 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
@@ -34,7 +34,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -79,7 +79,7 @@ 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
@@ -27,9 +27,7 @@ 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
@@ -11,7 +11,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest
-nf_core_version: 3.4.1
+nf_core_version: 3.5.1
 repository_type: pipeline
 template:
   author: "Harshil Patel, Phil Ewels, Rickard Hammarén"
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/CHANGELOG.md b/CHANGELOG.md
@@ -23,6 +23,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1622](https://github.com/nf-core/rnaseq/pull/1622) - Update tximeta/tximport module to fix sample name mangling
 - [PR #1620](https://github.com/nf-core/rnaseq/pull/1620) - Fix bigwig strand labeling for reverse-stranded libraries ([#1591](https://github.com/nf-core/rnaseq/issues/1591))
 - [PR #1621](https://github.com/nf-core/rnaseq/pull/1621) - Optimize qualimap performance with multi-threaded name sorting
+- [PR #1628](https://github.com/nf-core/rnaseq/pull/1628) - Template update for nf-core/tools v3.5.1
 
 ## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18
 
diff --git a/README.md b/README.md
@@ -5,13 +5,13 @@
   </picture>
 </h1>
 
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/rnaseq)
+[![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/rnaseq)
 [![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/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/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![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
@@ -396,7 +396,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf

Original file line number	Diff line number	Diff line change
`@@ -44,7 +44,7 @@ jobs:`
`44`	`44`	`}`
`45`	`45`	`profiles: test_full`
`46`	`46`
`47`		`- - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4`
	`47`	`+ - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5`
`48`	`48`	`with:`
`49`	`49`	`name: Seqera Platform debug log file`
`50`	`50`	`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: \|`