Update GitHub Actions

.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@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
+        uses: mshick/add-pr-comment@ec328af66588ab8f77cdeb2c264f14aba45bbf59 # v3
         with:
           message: |
             ## This PR is against the `main` branch :x:

.github/workflows/changelog.yml

@@ -31,7 +31,7 @@ jobs:
           PR_NUMBER="${{ github.event.issue.number }}"
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
@@ -60,12 +60,12 @@ jobs:
           echo "changed=$file_changed" >> $GITHUB_OUTPUT
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
       - name: Run pre-commit rules with prek
-        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2
         continue-on-error: true
         with:
           extra-args: --config .pre-commit-config.yaml --all-files

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

@@ -47,7 +47,7 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 

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

@@ -59,7 +59,7 @@ jobs:
         uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 

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

@@ -45,7 +45,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 

.github/workflows/deploy-pypi.yml

@@ -17,7 +17,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 

.github/workflows/fix-linting.yml

@@ -33,7 +33,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # 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@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Run prek
-        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2
         with:
           extra-args: --config .pre-commit-config.yaml --all-files

.github/workflows/nextflow-source-test.yml

@@ -20,7 +20,7 @@ jobs:
           path: nextflow
 
       - name: Set up Java
-        uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5
+        uses: actions/setup-java@1bcf9fb12cf4aa7d266a90ae39939e61372fe520 # v5
         with:
           distribution: "temurin"
           architecture: x64
@@ -45,7 +45,7 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 

.github/workflows/pytest.yml

@@ -76,7 +76,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: ${{ matrix.python-version }}
           token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/sync.yml

@@ -77,7 +77,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 

.github/workflows/update-template-snapshots.yml

@@ -56,7 +56,7 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 

.github/workflows/update-textual-snapshots.yml

@@ -37,7 +37,7 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 

nf_core/pipeline-template/.github/actions/nf-test/action.yml

@@ -25,7 +25,7 @@ runs:
         version: "{% raw %}${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
       with:
         python-version: "3.14"
 

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

@@ -21,7 +21,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
+        uses: mshick/add-pr-comment@ec328af66588ab8f77cdeb2c264f14aba45bbf59 # v3
         with:
           message: |
             ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:

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

@@ -47,7 +47,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
           architecture: "x64"

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@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # 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@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2
 
   nf-core:
     runs-on: ubuntu-latest
@@ -28,7 +28,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
           architecture: "x64"

nf_core/pipeline-template/.github/workflows/template-version-comment.yml

@@ -29,7 +29,7 @@ jobs:
         run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
-        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
+        uses: mshick/add-pr-comment@ec328af66588ab8f77cdeb2c264f14aba45bbf59 # v3
         if: |
           contains(env.OUTPUT, 'nf-core')
         with: