Update GitHub Actions

.github/workflows/changelog.yml

@@ -18,7 +18,7 @@ jobs:
           reaction: "eyes"
           stable_branch: "dev"
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 

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

@@ -42,7 +42,7 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out source-code repository
 
       # Set up nf-core/tools
@@ -52,7 +52,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
 

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

@@ -32,7 +32,7 @@ jobs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
       - name: checkout
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -56,15 +56,15 @@ jobs:
 
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
 

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

@@ -41,7 +41,7 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out source-code repository
 
       - name: Set up Python 3.14
@@ -50,7 +50,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
 

.github/workflows/deploy-pypi.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out source-code repository
 
       - name: Set up Python 3.14
@@ -22,7 +22,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
 

.github/workflows/fix-linting.yml

@@ -19,7 +19,7 @@ jobs:
           stable_branch: "dev"
 
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

.github/workflows/lint-code.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Run prek
         uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2

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

@@ -14,7 +14,7 @@ jobs:
 
     steps:
       - name: Check out Nextflow
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           repository: nextflow-io/nextflow
           path: nextflow
@@ -38,7 +38,7 @@ jobs:
           chmod +x $HOME/.local/bin/nextflow
           nextflow -version
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out nf-core/tools
         with:
           ref: dev
@@ -50,7 +50,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
 

.github/workflows/push_dockerhub.yml

@@ -34,10 +34,10 @@ jobs:
           swap-storage: true
 
       - name: Check out code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Set up QEMU for multi-architecture build
-        uses: docker/setup-qemu-action@ce360397dd3f832beb865e1373c09c0e9f86d70a # v4
+        uses: docker/setup-qemu-action@06116385d9baf250c9f4dcb4858b16962ea869c3 # v4
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@d7f5e7f509e45cec5c76c4d5afdd7de93d0b3df5 # v4
@@ -74,7 +74,7 @@ jobs:
               --push --no-cache .
 
       - name: Build and push nfcore/devcontainer image
-        uses: devcontainers/ci@b63b30de439b47a52267f241112c5b453b673db5 # v0.3
+        uses: devcontainers/ci@513af61f4de4f75d37e4438f184ba4358f0fc1ca # v0.3
         with:
           configFile: .devcontainer/build-devcontainer/devcontainer.json
           imageName: nfcore/devcontainer

.github/workflows/pytest.yml

@@ -40,7 +40,7 @@ jobs:
     name: Get test file matrix
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out source-code repository
 
       - name: List tests
@@ -72,7 +72,7 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
@@ -82,7 +82,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
 

.github/workflows/sync.yml

@@ -62,12 +62,12 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out nf-core/tools
         with:
           ref: ${{ github.ref_name }}
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
@@ -82,7 +82,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
 

.github/workflows/test_offline_configs.yml

@@ -53,11 +53,11 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out nf-core/tools
         with:
           ref: ${{ github.ref_name }}
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}

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

@@ -22,7 +22,7 @@ jobs:
           stable_branch: "dev"
 
       - name: checkout
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Create Matrix
         id: create_matrix
@@ -43,7 +43,7 @@ jobs:
       fail-fast: false
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -61,7 +61,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
 
@@ -145,7 +145,7 @@ jobs:
     runs-on: ubuntu-latest
     if: always() && needs.update-snapshots.result != 'skipped'
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

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

@@ -17,7 +17,7 @@ jobs:
           stable_branch: "dev"
 
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -42,7 +42,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
 

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

@@ -39,7 +39,7 @@ jobs:
     needs: configure
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3

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

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

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

@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
@@ -23,7 +23,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
@@ -34,7 +34,7 @@ jobs:
           architecture: "x64"
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0

nf_core/pipeline-template/.github/workflows/nf-test.yml

@@ -41,7 +41,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           fetch-depth: 0
 
@@ -87,7 +87,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           fetch-depth: 0
 

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

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         with:
           ref: ${{ github.event.pull_request.head.sha }}