Dev -> Master for 2.13

.github/actions/create-lint-wf/action.yml

@@ -0,0 +1,108 @@
+name: "Create and lint nf-core pipeline"
+description: "Create and lint nf-core pipeline"
+inputs:
+  NXF_VER:
+    description: "Nextflow version"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: go to subdirectory and change nextflow workdir
+      shell: bash
+      run: |
+        mkdir -p create-lint-wf
+        cd create-lint-wf
+        export NXF_WORK=$(pwd)
+
+    # Set up Nextflow
+    - name: Install Nextflow
+      uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+      with:
+        version: ${{ matrix.NXF_VER }}
+
+    # Build a pipeline from the template
+    - name: nf-core create
+      shell: bash
+      run: |
+        mkdir -p create-lint-wf && cd create-lint-wf
+        export NXF_WORK=$(pwd)
+        nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+
+    # Try syncing it before we change anything
+    - name: nf-core sync
+      shell: bash
+      run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
+      working-directory: create-lint-wf
+
+    # Run code style linting
+    - name: run pre-commit
+      shell: bash
+      run: pre-commit run --all-files
+      working-directory: create-lint-wf
+
+    # Update modules to the latest version
+    - name: nf-core modules update
+      shell: bash
+      run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
+      working-directory: create-lint-wf
+
+    # Remove TODO statements
+    - name: remove TODO
+      shell: bash
+      run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
+      working-directory: create-lint-wf
+
+    # Replace zenodo.XXXXXX to pass readme linting
+    - name: replace zenodo.XXXXXX
+      shell: bash
+      run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+      working-directory: create-lint-wf
+
+    # Run nf-core linting
+    - name: nf-core lint
+      shell: bash
+      run: nf-core --verbose --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
+      working-directory: create-lint-wf
+
+    - name: nf-core bump-version to release
+      shell: bash
+      run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
+      working-directory: create-lint-wf
+
+    - name: nf-core lint in release mode
+      shell: bash
+      run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
+      working-directory: create-lint-wf
+
+    - name: Upload log file artifact
+      if: ${{ always() }}
+      uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+      with:
+        name: nf-core-log-file-${{ matrix.NXF_VER }}
+        path: create-lint-wf/log.txt
+
+    - name: nf-core modules install
+      shell: bash
+      run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
+      working-directory: create-lint-wf
+
+    - name: nf-core modules install gitlab
+      shell: bash
+      run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
+      working-directory: create-lint-wf
+
+    - name: nf-core modules list local
+      shell: bash
+      run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
+      working-directory: create-lint-wf
+
+    - name: nf-core modules list remote
+      shell: bash
+      run: nf-core --log-file log.txt modules list remote
+      working-directory: create-lint-wf
+
+    - name: nf-core modules list remote gitlab
+      shell: bash
+      run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
+      working-directory: create-lint-wf

.github/workflows/branch.yml

@@ -18,7 +18,7 @@ jobs:
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v2
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:

.github/workflows/changelog.yml

@@ -17,7 +17,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
@@ -34,7 +34,7 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.11"
 
@@ -63,7 +63,7 @@ jobs:
           echo "File changed: ${{ env.changed }}"
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
           cache: "pip"

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v9
+      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
         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/create-lint-wf.yml

@@ -3,6 +3,9 @@ on:
   push:
     branches:
       - dev
+    paths-ignore:
+      - "docs/**"
+      - "CHANGELOG.md"
   pull_request:
   release:
     types: [published]
@@ -26,7 +29,7 @@ env:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -42,12 +45,12 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
           cache: pip
@@ -57,101 +60,30 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
 
-      # Set up Nextflow
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+      - name: run create-lint-wf
+        uses: ./.github/actions/create-lint-wf
         with:
-          version: ${{ matrix.NXF_VER }}
-
-      # Build a pipeline from the template
-      - name: nf-core create
-        run: |
-          mkdir create-lint-wf && cd create-lint-wf
-          export NXF_WORK=$(pwd)
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-
-      # Try syncing it before we change anything
-      - name: nf-core sync
-        run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
-        working-directory: create-lint-wf
+          NXF_VER: ${{ matrix.NXF_VER }}
 
       # Build a module from the template
       - name: nf-core modules create
-        run: nf-core --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta
-        working-directory: create-lint-wf
-
-      # Run code style linting
-      - name: run pre-commit
-        run: pre-commit run --all-files
-        working-directory: create-lint-wf
-
-      # Update modules to the latest version
-      - name: nf-core modules update
-        run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
+        run: nf-core --verbose --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta
         working-directory: create-lint-wf
 
       # Remove TODO statements
       - name: remove TODO
         run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
         working-directory: create-lint-wf
 
-      # Replace zenodo.XXXXXX to pass readme linting
-      - name: replace zenodo.XXXXXX
-        run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
-        working-directory: create-lint-wf
-
-      # Run nf-core linting
-      - name: nf-core lint
-        run: nf-core --verbose --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
-        working-directory: create-lint-wf
-
       # Run the other nf-core commands
       - name: nf-core list
         run: nf-core --log-file log.txt list
         working-directory: create-lint-wf
 
-      # - name: nf-core licences
-      #   run: nf-core --log-file log.txt licences nf-core-testpipeline
-
       - name: nf-core schema
         run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts
         working-directory: create-lint-wf
 
-      - name: nf-core bump-version
-        run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
-        working-directory: create-lint-wf
-
-      - name: nf-core lint in release mode
-        run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
-        working-directory: create-lint-wf
-
-      - name: nf-core modules install
-        run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
-        working-directory: create-lint-wf
-
-      - name: nf-core modules install gitlab
-        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
-        working-directory: create-lint-wf
-
-      - name: nf-core modules list local
-        run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
-        working-directory: create-lint-wf
-
-      - name: nf-core modules list remote
-        run: nf-core --log-file log.txt modules list remote
-        working-directory: create-lint-wf
-
-      - name: nf-core modules list remote gitlab
-        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
-        working-directory: create-lint-wf
-
-      - name: Upload log file artifact
-        if: ${{ always() }}
-        uses: actions/upload-artifact@v4
-        with:
-          name: nf-core-log-file-${{ matrix.NXF_VER }}
-          path: create-lint-wf/log.txt
-
       - name: Cleanup work directory
         run: sudo rm -rf create-lint-wf
         if: always()

.github/workflows/create-test-lint-wf-template.yml

@@ -39,7 +39,8 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
         runner:
-          - ${{ github.event.inputs.runners || 'self-hosted' }}
+          # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
+          - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
         profile: ["self_hosted_runner"]
         include:
           - TEMPLATE: "template_skip_all.yml"
@@ -57,11 +58,11 @@ jobs:
           cd create-lint-wf-template
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
 
@@ -71,7 +72,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
         with:
           version: latest-everything
 
@@ -154,7 +155,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: nf-core-log-file-${{ matrix.TEMPLATE }}
           path: create-test-lint-wf/artifact_files.tar

.github/workflows/create-test-wf.yml

@@ -3,6 +3,9 @@ on:
   push:
     branches:
       - dev
+    paths-ignore:
+      - "docs/**"
+      - "CHANGELOG.md"
   pull_request:
   release:
     types: [published]
@@ -26,7 +29,8 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -41,11 +45,11 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
 
@@ -55,7 +59,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
         with:
           version: ${{ matrix.NXF_VER }}
 
@@ -68,7 +72,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-test-wf/log.txt