Added a test for invalid files #23
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name: nf-core linting | |
# This workflow is triggered on pushes and PRs to the repository. | |
# It runs the `nf-core 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@v4 | |
- name: Set up Python 3.11 | |
uses: actions/setup-python@v5 | |
with: | |
python-version: 3.11 | |
cache: "pip" | |
- 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@v4 | |
# - name: Install Nextflow | |
# uses: nf-core/setup-nextflow@v1 | |
# - uses: actions/setup-python@v5 | |
# with: | |
# python-version: "3.11" | |
# architecture: "x64" | |
# - name: Install dependencies | |
# run: | | |
# python -m pip install --upgrade pip | |
# pip install nf-core | |
# - name: Run nf-core lint | |
# 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 lint --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@v4 | |
# with: | |
# name: linting-logs | |
# path: | | |
# lint_log.txt | |
# lint_results.md | |
# PR_number.txt |