updated workflows

.github/workflows/linting.yml

@@ -1,7 +1,7 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
-# that the code meets the nf-core guidelines.
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
+# that the code meets the nf-core guidelines. {%- raw %}
 on:
   push:
     branches:
@@ -14,41 +14,54 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
 
       - name: Run pre-commit
-        #run: pre-commit run --all-files
-        run: pre-commit run --files nf-test.config
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/[email protected]
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -61,10 +74,10 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
             lint_log.txt
             lint_results.md
-            PR_number.txt
+            PR_number.txt {%- endraw %}

.github/workflows/linting_comment.yml

@@ -1,6 +1,6 @@
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
-# It posts an automated comment to the PR, even if the PR is coming from a fork
+# It posts an automated comment to the PR, even if the PR is coming from a fork {%- raw %}
 
 on:
   workflow_run:
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -25,4 +25,4 @@ jobs:
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
-          path: linting-logs/lint_results.md
+          path: linting-logs/lint_results.md {%- endraw %}