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run nf-core lint --release on PRs to master #3148

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merged 5 commits into from
Sep 6, 2024
Merged

run nf-core lint --release on PRs to master #3148

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21e03ec
run nf-core lint --release on PRs to master
mirpedrol Aug 30, 2024
424743e
udpate changelog
mirpedrol Aug 30, 2024
6b3e848
Don't look for dev, look for not master
ewels Sep 6, 2024
3e020cf
Move if statements to top of YAML blocks
ewels Sep 6, 2024
4f31818
Merge branch 'dev' into lint-release
ewels Sep 6, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@
- add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
- add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
- add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
- run nf-core lint `--release` on PRs to master ([#3148](https://github.com/nf-core/tools/pull/3148))
- Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))

### Linting
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9 changes: 9 additions & 0 deletions nf_core/pipeline-template/.github/workflows/linting.yml
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Expand Up @@ -53,12 +53,21 @@ jobs:
pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}

- name: Run nf-core pipelines lint
if: ${{ github.base_ref != 'master' }}
env:
GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md

- name: Run nf-core pipelines lint --release
if: ${{ github.base_ref == 'master' }}
env:
GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md

- name: Save PR number
if: ${{ always() }}
run: echo ${{ github.event.pull_request.number }} > PR_number.txt
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