chore(deps): update github actions

.github/workflows/changelog.yml

@@ -19,7 +19,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
@@ -36,7 +36,7 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -65,7 +65,7 @@ jobs:
           echo "File changed: ${{ env.changed }}"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"

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

@@ -48,12 +48,12 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: pip

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

@@ -40,7 +40,7 @@ jobs:
       - name: 🏗 Set up yq
         uses: frenck/action-setup-yq@v1
       - name: checkout
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -77,11 +77,11 @@ jobs:
           cd create-lint-wf-template
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 

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

@@ -48,11 +48,11 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 

.github/workflows/deploy-pypi.yml

@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 

.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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 

.github/workflows/lint-code.yml

@@ -18,10 +18,10 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"

.github/workflows/push_dockerhub_dev.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev

.github/workflows/push_dockerhub_release.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest

.github/workflows/pytest.yml

@@ -61,7 +61,7 @@ jobs:
     name: Get test file matrix
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: List tests
@@ -87,11 +87,11 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -172,9 +172,9 @@ jobs:
           mkdir -p pytest
           cd pytest
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:

.github/workflows/sync.yml

@@ -60,10 +60,10 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
@@ -73,7 +73,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 

.github/workflows/update-textual-snapshots.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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -33,7 +33,7 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"

.github/workflows/update_components_template.yml

@@ -11,10 +11,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.x"
 

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

@@ -45,7 +45,7 @@ jobs:
             profile: "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2

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

@@ -35,7 +35,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"

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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 

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

@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,12 +31,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"

nf_core/pipeline-template/.github/workflows/release-announcements.yml

@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.10"
       - name: Install dependencies

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@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}