make creat-lint-wf composable and regularly update components in template

.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@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: ${{ always() }}
+      uses: actions/upload-artifact@v4
+      with:
+        name: nf-core-log-file-${{ 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/create-lint-wf.yml

@@ -3,6 +3,9 @@ on:
   push:
     branches:
       - dev
+    paths-ignore:
+      - "docs/**"
+      - "CHANGELOG.md"
   pull_request:
   release:
     types: [published]
@@ -57,101 +60,30 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
 
-      # Set up Nextflow
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@dccbf847604cbc34610280d79644a02035d924ac # 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: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
-        with:
-          name: nf-core-log-file-${{ 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

@@ -3,6 +3,9 @@ on:
   push:
     branches:
       - dev
+    paths-ignore:
+      - "docs/**"
+      - "CHANGELOG.md"
     paths:
       - nf_core/pipeline-template/**
   pull_request:

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

@@ -3,6 +3,9 @@ on:
   push:
     branches:
       - dev
+    paths-ignore:
+      - "docs/**"
+      - "CHANGELOG.md"
   pull_request:
   release:
     types: [published]

.github/workflows/pytest.yml

@@ -12,6 +12,7 @@ on:
     paths-ignore:
       - "docs/**"
       - "CHANGELOG.md"
+      - ".github/**"
   release:
     types: [published]
   workflow_dispatch:

.github/workflows/update_components_template.yml

@@ -0,0 +1,46 @@
+name: Update Modules Template
+
+on:
+  schedule:
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+
+jobs:
+  update_modules:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - name: Install nf-core
+        run: pip install nf-core
+
+      - name: Update modules
+        run: nf-core modules update --all
+        working-directory: nf-core/pipeline-template
+
+      - name: Update subworkflows
+        run: nf-core subworkflows update --all
+        working-directory: nf-core/pipeline-template
+
+      # Commit the changes
+      - name: Commit changes
+        run: |
+          git config user.email "[email protected]"
+          git config user.name "nf-core-bot"
+          git add .
+          git status
+          git commit -m "[automated] Fix code linting"
+
+      # Open a new PR to dev with the changes
+      - name: Create PR
+        run: |
+          git checkout -b update-modules
+          git push origin update-modules
+          gh pr create --title "Update modules in template" --body "This PR updates the modules in the pipeline template" --base dev --head update-modules

CHANGELOG.md

@@ -9,6 +9,8 @@
 
 ### Linting
 
+- make creat-lint-wf composable ([#2733](https://github.com/nf-core/tools/pull/2733))
+
 ### Modules
 
 ### General

nf_core/lint/multiqc_config.py

@@ -9,6 +9,7 @@ def multiqc_config(self) -> Dict[str, List[str]]:
     Basic template:
 
     .. code-block:: yaml
+
         report_comment: >
             This report has been generated by the <a href="https://github.com/nf-core/quantms" target="_blank">nf-core/quantms</a>
             analysis pipeline. For information about how to interpret these results, please see the
@@ -18,8 +19,8 @@ def multiqc_config(self) -> Dict[str, List[str]]:
                 order: -1000
             nf-core-quantms-summary:
                 order: -1001
-
         export_plots: true
+
     """
     passed: List[str] = []
     failed: List[str] = []