Update actions/checkout action to v6

.github/workflows/changelog.yml

@@ -19,7 +19,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # 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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out source-code repository
 
       # Set up nf-core/tools

.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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -56,7 +56,7 @@ jobs:
 
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6

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

@@ -41,7 +41,7 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out source-code repository
 
       - name: Set up Python 3.14

.github/workflows/deploy-pypi.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out source-code repository
 
       - name: Set up Python 3.14

.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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

.github/workflows/lint-code.yml

@@ -20,7 +20,7 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6

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

@@ -14,12 +14,12 @@ jobs:
 
     steps:
       - name: Check out Nextflow
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           repository: nextflow-io/nextflow
           path: nextflow
 
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out nf-core/tools
         with:
           ref: dev

.github/workflows/push_dockerhub_dev.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
       - name: Set up QEMU for multi-architecture build
         uses: docker/setup-qemu-action@c7c53464625b32c7a7e944ae62b3e17d2b600130 # v3

.github/workflows/push_dockerhub_release.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
       - name: Set up QEMU for multi-architecture build
         uses: docker/setup-qemu-action@c7c53464625b32c7a7e944ae62b3e17d2b600130 # v3

.github/workflows/pytest.yml

@@ -35,7 +35,7 @@ jobs:
     name: Get test file matrix
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out source-code repository
 
       - name: List tests
@@ -64,7 +64,7 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
@@ -138,7 +138,7 @@ jobs:
       - runs-on=${{ github.run_id }}-coverage
       - runner=2cpu-linux-x64
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:

.github/workflows/sync.yml

@@ -62,12 +62,12 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out nf-core/tools
         with:
           ref: ${{ github.ref_name }}
 
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}

.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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out nf-core/tools
         with:
           ref: ${{ github.ref_name }}
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}

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

@@ -17,7 +17,7 @@ jobs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
       - name: checkout
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
       - name: Create Matrix
         id: create_matrix
@@ -36,7 +36,7 @@ jobs:
       fail-fast: false
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

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

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # 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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2

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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           fetch-depth: 0
 
@@ -87,7 +87,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # 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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           ref: ${{ github.event.pull_request.head.sha }}