Update GitHub Actions

renovate[bot] · web-flow · commit 41d3cefeee83 · 2026-04-27T09:15:22.000Z
diff --git a/.github/workflows/branch.yml b/.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@64b8e914979889d746c99dea15a76e77ef64580a # v3
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         with:
           message: |
             ## This PR is against the `main` branch :x:
diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
@@ -72,7 +72,7 @@ jobs:
           python-version: "3.14"
 
       - name: Run pre-commit rules with prek
-        uses: j178/prek-action@53276d8b0d10f8b6672aa85b4588c6921d0370cc # v2
+        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
         continue-on-error: true
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -77,7 +77,7 @@ jobs:
           version: latest-everything
 
       - name: Install nf-test
-        uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+        uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
         with:
           version: "0.9.4"
           install-pdiff: true
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -63,7 +63,7 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       - name: Install nf-test
-        uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+        uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
         with:
           version: "0.9.4"
           install-pdiff: true
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -33,7 +33,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@53276d8b0d10f8b6672aa85b4588c6921d0370cc # v2
+        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
         continue-on-error: true
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -22,6 +22,6 @@ jobs:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Run prek
-        uses: j178/prek-action@53276d8b0d10f8b6672aa85b4588c6921d0370cc # v2
+        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
diff --git a/.github/workflows/push_dockerhub.yml b/.github/workflows/push_dockerhub.yml
@@ -74,7 +74,7 @@ jobs:
               --push --no-cache .
 
       - name: Build and push nfcore/devcontainer image
-        uses: devcontainers/ci@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 # v0.3
+        uses: devcontainers/ci@b63b30de439b47a52267f241112c5b453b673db5 # v0.3
         with:
           configFile: .devcontainer/build-devcontainer/devcontainer.json
           imageName: nfcore/devcontainer
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -95,7 +95,7 @@ jobs:
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - name: Install nf-test
-        uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+        uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
 
       - name: move coveragerc file up
         run: |
diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml
@@ -74,7 +74,7 @@ jobs:
           version: latest-everything
 
       - name: Install nf-test
-        uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+        uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
         with:
           version: "0.9.4"
           install-pdiff: true
diff --git a/nf_core/pipeline-template/.github/actions/get-shards/action.yml b/nf_core/pipeline-template/.github/actions/get-shards/action.yml
@@ -21,7 +21,7 @@ runs:
   using: "composite"
   steps:
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: ${{ env.NFT_VER }}
     - name: Get number of shards
diff --git a/nf_core/pipeline-template/.github/actions/nf-test/action.yml b/nf_core/pipeline-template/.github/actions/nf-test/action.yml
@@ -30,7 +30,7 @@ runs:
         python-version: "3.14"
 
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: "${{ env.NFT_VER }}"
         install-pdiff: true
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -23,7 +23,7 @@ jobs:
           echo "revision={%- raw -%}${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Seqera Platform CLI tool action {%- raw %}
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         with:
           workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
diff --git a/nf_core/pipeline-template/.github/workflows/branch.yml b/nf_core/pipeline-template/.github/workflows/branch.yml
@@ -21,7 +21,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@64b8e914979889d746c99dea15a76e77ef64580a # v3
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         with:
           message: |
             ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
diff --git a/nf_core/pipeline-template/.github/workflows/fix_linting.yml b/nf_core/pipeline-template/.github/workflows/fix_linting.yml
@@ -34,7 +34,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@53276d8b0d10f8b6672aa85b4588c6921d0370cc # v2
+        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
         continue-on-error: true
 
       # indication that the linting has finished
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Run prek
-        uses: j178/prek-action@53276d8b0d10f8b6672aa85b4588c6921d0370cc # v2
+        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
@@ -31,7 +31,7 @@ jobs:
           architecture: "x64"
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
 
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
diff --git a/nf_core/pipeline-template/.github/workflows/template-version-comment.yml b/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@64b8e914979889d746c99dea15a76e77ef64580a # v3
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         if: |
           contains(env.OUTPUT, 'nf-core')
         with:
