Pinning verison of nf-core and bug fixes

.github/workflows/linting.yml

@@ -11,106 +11,64 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - uses: actions/setup-node@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          node-version: "20.11.0"
+          python-version: "3.12"
 
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
-
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-node@v3
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  PythonBlack:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # 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@v1
-        with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: read .nf-core.yml
         uses: pietrobolcato/[email protected]
         id: read_yml
         with:
-          config: ${{ github.workspace }}/.nf-core.yaml
+          config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
-      - name: Run nf-core lint
-        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 lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
-
-      - name: Save PR number
-        if: ${{ always() }}
-        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
-
-      - name: Upload linting log file artifact
-        if: ${{ always() }}
-        uses: actions/upload-artifact@v3
-        with:
-          name: linting-logs
-          path: |
-            lint_log.txt
-            lint_results.md
-            PR_number.txt
+          - name: Run nf-core lint
+          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 lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+  
+        - name: Save PR number
+          if: ${{ always() }}
+          run: echo ${{ github.event.pull_request.number }} > PR_number.txt
+  
+        - name: Upload linting log file artifact
+          if: ${{ always() }}
+          uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+          with:
+            name: linting-logs
+            path: |
+              lint_log.txt
+              lint_results.md
+              PR_number.txt {%- endraw %}