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Update GitHub Actions
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renovate[bot] authored Oct 24, 2024
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6 changes: 3 additions & 3 deletions .github/workflows/changelog.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
)
steps:
- uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
with:
token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}

Expand All @@ -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"

Expand Down Expand Up @@ -65,7 +65,7 @@ jobs:
echo "File changed: ${{ env.changed }}"
- name: Set up Python 3.12
uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
with:
python-version: "3.12"
cache: "pip"
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4 changes: 2 additions & 2 deletions .github/workflows/create-lint-wf.yml
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Expand Up @@ -48,12 +48,12 @@ jobs:
export NXF_WORK=$(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
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6 changes: 3 additions & 3 deletions .github/workflows/create-test-lint-wf-template.yml
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Expand Up @@ -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: |
Expand Down Expand Up @@ -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"

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4 changes: 2 additions & 2 deletions .github/workflows/create-test-wf.yml
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Expand Up @@ -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"

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4 changes: 2 additions & 2 deletions .github/workflows/deploy-pypi.yml
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Expand Up @@ -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"

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4 changes: 2 additions & 2 deletions .github/workflows/fix-linting.yml
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Expand Up @@ -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 }}

Expand All @@ -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"

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4 changes: 2 additions & 2 deletions .github/workflows/lint-code.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion .github/workflows/push_dockerhub_dev.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .github/workflows/push_dockerhub_release.yml
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Expand Up @@ -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
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10 changes: 5 additions & 5 deletions .github/workflows/pytest.yml
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Expand Up @@ -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
Expand All @@ -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"
Expand Down Expand Up @@ -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:
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6 changes: 3 additions & 3 deletions .github/workflows/sync.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}
Expand All @@ -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"

Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/update-textual-snapshots.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}

Expand All @@ -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"
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4 changes: 2 additions & 2 deletions .github/workflows/update_components_template.yml
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Expand Up @@ -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"

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2 changes: 1 addition & 1 deletion nf_core/pipeline-template/.github/workflows/ci.yml
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Expand Up @@ -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
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down
4 changes: 2 additions & 2 deletions nf_core/pipeline-template/.github/workflows/fix-linting.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}

Expand All @@ -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"

Expand Down
8 changes: 4 additions & 4 deletions nf_core/pipeline-template/.github/workflows/linting.yml
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Expand Up @@ -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"

Expand All @@ -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"
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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Original file line number Diff line number Diff line change
Expand Up @@ -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 }}

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