chore(deps): update github actions

nf-core · Apr 24, 2024 · 9bfdcee · 9bfdcee
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commit 9bfdcee
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Showing 17 changed files with 27 additions and 27 deletions.
diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml
@@ -77,7 +77,7 @@ runs:
 
  - name: Upload log file artifact
  if: ${{ always() }}
- uses: actions/upload-artifact@1746f4ab65b179e0ea60a494b83293b640dd5bba # v4
+ uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
  with:
  name: nf-core-log-file-${{ matrix.NXF_VER }}
  path: create-lint-wf/log.txt

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
@@ -19,7 +19,7 @@ jobs:
  )
 
  steps:
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  with:
  token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -48,7 +48,7 @@ jobs:
  export NXF_WORK=$(pwd)
 
  # Get the repo code
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  name: Check out source-code repository
 
  # Set up nf-core/tools

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  name: Check out source-code repository
 
  - name: Set up Python 3.12
@@ -158,7 +158,7 @@ jobs:
 
  - name: Upload log file artifact
  if: ${{ always() }}
- uses: actions/upload-artifact@1746f4ab65b179e0ea60a494b83293b640dd5bba # v4
+ uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
  with:
  name: nf-core-log-file-${{ matrix.TEMPLATE }}
  path: create-test-lint-wf/artifact_files.tar

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -48,7 +48,7 @@ jobs:
  cd create-test-wf
  export NXF_WORK=$(pwd)
 
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  name: Check out source-code repository
 
  - name: Set up Python 3.12
@@ -75,7 +75,7 @@ jobs:
 
  - name: Upload log file artifact
  if: ${{ always() }}
- uses: actions/upload-artifact@1746f4ab65b179e0ea60a494b83293b640dd5bba # v4
+ uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
  with:
  name: nf-core-log-file-${{ matrix.NXF_VER }}
  path: create-test-wf/log.txt

diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
@@ -13,7 +13,7 @@ jobs:
  runs-on: ubuntu-latest
 
  steps:
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  name: Check out source-code repository
 
  - name: Set up Python 3.12

diff --git a/.github/workflows/fix-linting.yml b/.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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  with:
  token: ${{ secrets.nf_core_bot_auth_token }}
 

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -18,7 +18,7 @@ jobs:
  env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  steps:
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
 
  - name: Set up Python 3.12
  uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
@@ -23,7 +23,7 @@ jobs:
  fail-fast: false
  steps:
  - name: Check out code
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
 
  - name: Build nfcore/tools:dev docker image
  run: docker build --no-cache . -t nfcore/tools:dev

diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
@@ -23,7 +23,7 @@ jobs:
  fail-fast: false
  steps:
  - name: Check out code
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
 
  - name: Build nfcore/tools:latest docker image
  run: docker build --no-cache . -t nfcore/tools:latest

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -61,7 +61,7 @@ jobs:
  name: Get test file matrix
  runs-on: "ubuntu-latest"
  steps:
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  name: Check out source-code repository
 
  - name: List tests
@@ -87,7 +87,7 @@ jobs:
  cd pytest
  export NXF_WORK=$(pwd)
 
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  name: Check out source-code repository
 
  - name: Set up Python ${{ needs.setup.outputs.python-version }}
@@ -143,7 +143,7 @@ jobs:
  fi
 
  - name: Upload coverage
- uses: actions/upload-artifact@1746f4ab65b179e0ea60a494b83293b640dd5bba # v4
+ uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
  with:
  name: coverage_${{ matrix.test }}
  path: .coverage
@@ -158,7 +158,7 @@ jobs:
  mkdir -p pytest
  cd pytest
 
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # 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@8caf195ad4b1dee92908e23f56eeb0696f1dd42d # v4
+ uses: actions/download-artifact@9c19ed7fe5d278cd354c7dfd5d3b88589c7e2395 # v4
  - name: Run coverage
  run: |
  coverage combine --keep coverage*/.coverage*

diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
@@ -6,7 +6,7 @@ jobs:
  runs-on: ubuntu-latest
  steps:
  - name: Check out the repo
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  - name: Set up Python
  uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
  with:

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -44,10 +44,10 @@ jobs:
  matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
  fail-fast: false
  steps:
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  name: Check out nf-core/tools
 
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  name: Check out nf-core/${{ matrix.pipeline }}
  with:
  repository: nf-core/${{ matrix.pipeline }}
@@ -86,7 +86,7 @@ jobs:
 
  - name: Upload sync log file artifact
  if: ${{ always() }}
- uses: actions/upload-artifact@1746f4ab65b179e0ea60a494b83293b640dd5bba # v4
+ uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
  with:
  name: sync_log_${{ matrix.pipeline }}
  path: sync_log_${{ matrix.pipeline }}.txt
diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml
@@ -11,7 +11,7 @@ jobs:
 
  steps:
  - name: Checkout repository
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
 
  - name: Set up Python
  uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5

diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
  - "latest-everything"
  steps:
  - name: Check out pipeline code
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
 
  - name: Install Nextflow
  uses: nf-core/setup-nextflow@v2

diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
  with:
  token: ${{ secrets.nf_core_bot_auth_token }}
 

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:
  pre-commit:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # 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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+ uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4
 
  - name: Install Nextflow
  uses: nf-core/setup-nextflow@v2
@@ -60,7 +60,7 @@ jobs:
 
  - name: Upload linting log file artifact
  if: ${{ always() }}
- uses: actions/upload-artifact@1746f4ab65b179e0ea60a494b83293b640dd5bba # v4
+ uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
  with:
  name: linting-logs
  path: |