Dev -> master for nf-core/rnaseq 3.22.0

.devcontainer/devcontainer.json

@@ -1,20 +1,20 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
 
-    // Configure tool-specific properties.
-    "customizations": {
-        // Configure properties specific to VS Code.
-        "vscode": {
-            // Set *default* container specific settings.json values on container create.
-            "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python"
-            },
+    "remoteUser": "root",
+    "privileged": true,
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }

.devcontainer/setup.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Update welcome message
+echo "Welcome to the nf-core/rnaseq devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.github/actions/nf-test/action.yml

@@ -25,9 +25,9 @@ runs:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
       with:
-        python-version: "3.13"
+        python-version: "3.14"
 
     - name: Install nf-test
       uses: nf-core/setup-nf-test@v1
@@ -52,6 +52,8 @@ runs:
       with:
         auto-update-conda: true
         conda-solver: libmamba
+        channels: conda-forge
+        channel-priority: strict
         conda-remove-defaults: true
 
     # Set up secrets

.github/workflows/awsfulltest.yml

@@ -31,22 +31,22 @@ jobs:
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnaseq/work-${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/rnaseq/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "aligner": "${{ matrix.aligner }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ steps.revision.outputs.revision }}/aligner_${{ matrix.aligner }}/"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/rnaseq/results-${{ steps.revision.outputs.revision }}/aligner_${{ matrix.aligner }}/"
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -14,20 +14,20 @@ jobs:
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnaseq/work-${{ github.sha }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/rnaseq/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/rnaseq/results-test-${{ github.sha }}"
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/download_pipeline.yml

@@ -44,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -57,7 +57,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git@dev
+          pip install git+https://github.com/nf-core/tools.git
 
       - name: Make a cache directory for the container images
         run: |
@@ -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*

.github/workflows/fix_linting.yml

@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
       # indication that the linting is being fixed
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -47,7 +47,7 @@ jobs:
       # indication that the linting has finished
       - name: react if linting finished succesfully
         if: steps.pre-commit.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: "+1"
@@ -67,21 +67,21 @@ jobs:
       - name: react if linting errors were fixed
         id: react-if-fixed
         if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: hooray
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: confused
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |

.github/workflows/linting.yml

@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
@@ -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: |

.github/workflows/linting_comment.yml

@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.github/workflows/nf-test.yml

@@ -1,12 +1,6 @@
 name: Run nf-test
 on:
   pull_request:
-    paths-ignore:
-      - "docs/**"
-      - "**/meta.yml"
-      - "**/*.md"
-      - "**/*.png"
-      - "**/*.svg"
   release:
     types: [published]
   workflow_dispatch:
@@ -18,9 +12,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_DIFF: "pdiff"
-  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
-  NFT_VER: "0.9.2"
+  NFT_VER: "0.9.3"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -42,7 +34,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -80,14 +72,14 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.10.5"
+          - "25.04.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -101,6 +93,7 @@ jobs:
           SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
           SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
           SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
+          NXF_VERSION: ${{ matrix.NXF_VER }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
@@ -122,7 +115,7 @@ jobs:
           fi
 
   confirm-pass:
-    needs: [nf-test]
+    needs: [nf-test-changes, nf-test]
     if: always()
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-confirm-pass
@@ -143,7 +136,7 @@ jobs:
       - name: debug-print
         if: always()
         run: |
-          echo "::group::DEBUG: `needs` Contents"
+          echo "::group::DEBUG: needs Contents"
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "::endgroup::"

.github/workflows/release-announcements.yml

@@ -14,6 +14,11 @@ jobs:
         run: |
           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_description
+        run: |
+          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 }}
@@ -22,7 +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_description.outputs.description }}
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics

.github/workflows/template-version-comment.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}