Adressing review suggestions for Version 1.0.0 #33
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name: nf-core linting | |
# This workflow is triggered on pushes and PRs to the repository. | |
# It runs the `nf-core pipelines lint` and markdown lint tests to ensure | |
# that the code meets the nf-core guidelines. | |
on: | |
push: | |
branches: | |
- dev | |
pull_request: | |
release: | |
types: [published] | |
jobs: | |
pre-commit: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
- name: Set up Python 3.12 | |
uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
with: | |
python-version: "3.12" | |
- name: Install pre-commit | |
run: pip install pre-commit | |
- name: Run pre-commit | |
run: pre-commit run --all-files | |
nf-core: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
with: | |
python-version: "3.12" | |
architecture: "x64" | |
- name: read .nf-core.yml | |
uses: pietrobolcato/[email protected] | |
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'] }} | |
- 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 | |
- name: Upload linting log file artifact | |
if: ${{ always() }} | |
uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 | |
with: | |
name: linting-logs | |
path: | | |
lint_log.txt | |
lint_results.md | |
PR_number.txt |