Update GitHub Actions

.github/workflows/changelog.yml

@@ -19,7 +19,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 

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

@@ -48,7 +48,7 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
       # Set up nf-core/tools

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

@@ -61,7 +61,7 @@ jobs:
           cd create-lint-wf-template
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12

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

@@ -48,7 +48,7 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12

.github/workflows/deploy-pypi.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
       - name: Set up Python 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@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

.github/workflows/lint-code.yml

@@ -18,7 +18,7 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5

.github/workflows/push_dockerhub_dev.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # 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@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # 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@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
       - name: List tests
@@ -87,7 +87,7 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
@@ -158,7 +158,7 @@ jobs:
           mkdir -p pytest
           cd pytest
 
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
       - name: Set up Python 3.12
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         env:
@@ -177,7 +177,7 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@9c19ed7fe5d278cd354c7dfd5d3b88589c7e2395 # v4
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*

.github/workflows/rich-codex.yml

@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
       - name: Set up Python
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:

.github/workflows/sync.yml

@@ -44,10 +44,10 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}

.github/workflows/update_components_template.yml

@@ -11,7 +11,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Set up Python
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5

CHANGELOG.md

@@ -60,6 +60,7 @@
 - Update GitHub Actions ([#2927](https://github.com/nf-core/tools/pull/2927))
 - Update gitpod/workspace-base Docker digest to 5aeb24f ([#2929](https://github.com/nf-core/tools/pull/2929))
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.10.0 ([#2933](https://github.com/nf-core/tools/pull/2933))
+- Update GitHub Actions ([#2939](https://github.com/nf-core/tools/pull/2939))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
 

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

@@ -28,7 +28,7 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2

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@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

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

@@ -14,7 +14,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2