Update GitHub Actions

.github/workflows/changelog.yml

@@ -65,7 +65,7 @@ jobs:
           python-version: "3.14"
 
       - name: Run pre-commit rules with prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
         continue-on-error: true
         with:
           extra-args: --config .pre-commit-config.yaml --all-files

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@eb5cf3af3ac0a1aa4c9c45633dd1ae542a27a899 # 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/fix-linting.yml

@@ -33,7 +33,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
         continue-on-error: true

.github/workflows/lint-code.yml

@@ -22,6 +22,6 @@ jobs:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Run prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
         with:
           extra-args: --config .pre-commit-config.yaml --all-files

.github/workflows/pytest.yml

@@ -128,7 +128,7 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: always()
-        uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6
+        uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6
         with:
           files: ./coverage.xml
           flags: python-${{ matrix.python-version }}

nf_core/pipeline-template/.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@eb5cf3af3ac0a1aa4c9c45633dd1ae542a27a899 # 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."

nf_core/pipeline-template/.github/workflows/fix_linting.yml

@@ -37,7 +37,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
         continue-on-error: true
 
       # indication that the linting has finished

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -17,7 +17,7 @@ jobs:
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - name: Run prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
 
   nf-core:
     runs-on: ubuntu-latest