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Merged
dialvarezs merged 5 commits into from
Dec 11, 2025
Merged

Switch to uv and prek on pipeline linting #3942

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636d663
Use uv and prek on pipeline linting
dialvarezs Nov 30, 2025
523ffeb
Merge branch 'dev' into modernize-pipeline-linting
dialvarezs Dec 3, 2025
7c0b6ce
Merge branch 'dev' into modernize-pipeline-linting
mashehu Dec 11, 2025
87f8c66
Update nf_core/pipeline-template/.github/workflows/linting.yml
dialvarezs Dec 11, 2025
8758837
Fix github action syntax
dialvarezs Dec 11, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,8 @@

### Template

- switch to uv and prek for pipeline linting workflow ([#3942](https://github.com/nf-core/tools/pull/3942))

### Linting

- fix test for linting for version.yml ([#3947](https://github.com/nf-core/tools/pull/3947))
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19 changes: 7 additions & 12 deletions nf_core/pipeline-template/.github/workflows/linting.yml
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Expand Up @@ -13,16 +13,10 @@ jobs:
steps:
- uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6

- name: Set up Python 3.14
uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
- name: Run prek
uses: j178/prek-action@91fd7d7cf70ae1dee9f4f44e7dfa5d1073fe6623 # v1.0.11
with:
python-version: "3.14"

- name: Install pre-commit
run: pip install pre-commit

- name: Run pre-commit
run: pre-commit run --all-files
extra-args: "--all-files"

nf-core:
runs-on: ubuntu-latest
Expand All @@ -38,16 +32,17 @@ jobs:
python-version: "3.14"
architecture: "x64"

- name: Setup uv
uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4

- name: read .nf-core.yml
uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
id: read_yml
with:
config: ${{ github.workspace }}/.nf-core.yml

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}

- name: Run nf-core pipelines lint
if: ${{ github.base_ref != 'master' }}
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