Implement nf-test for rank variants #154
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| name: Fix linting from a comment | |
| on: | |
| issue_comment: | |
| types: [created] | |
| jobs: | |
| fix-linting: | |
| # Only run if comment is on a PR with the main repo, and if it contains the magic keywords | |
| if: > | |
| contains(github.event.comment.html_url, '/pull/') && | |
| contains(github.event.comment.body, '@nf-core-bot fix linting') && | |
| github.repository == 'genomic-medicine-sweden/nallo' | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Use the @nf-core-bot token to check out so we can push later | |
| - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| token: ${{ secrets.nf_core_bot_auth_token }} | |
| # indication that the linting is being fixed | |
| - name: React on comment | |
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: eyes | |
| # Action runs on the issue comment, so we don't get the PR by default | |
| # Use the gh cli to check out the PR | |
| - name: Checkout Pull Request | |
| run: gh pr checkout ${{ github.event.issue.number }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | |
| # Install and run pre-commit | |
| - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install pre-commit | |
| run: pip install pre-commit | |
| - name: Run pre-commit | |
| id: pre-commit | |
| run: pre-commit run --all-files | |
| continue-on-error: true | |
| # indication that the linting has finished | |
| - name: react if linting finished succesfully | |
| if: steps.pre-commit.outcome == 'success' | |
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: "+1" | |
| - name: Commit & push changes | |
| id: commit-and-push | |
| if: steps.pre-commit.outcome == 'failure' | |
| run: | | |
| git config user.email "[email protected]" | |
| git config user.name "nf-core-bot" | |
| git config push.default upstream | |
| git add . | |
| git status | |
| git commit -m "[automated] Fix code linting" | |
| git push | |
| - name: react if linting errors were fixed | |
| id: react-if-fixed | |
| if: steps.commit-and-push.outcome == 'success' | |
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: hooray | |
| - name: react if linting errors were not fixed | |
| if: steps.commit-and-push.outcome == 'failure' | |
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: confused | |
| - name: react if linting errors were not fixed | |
| if: steps.commit-and-push.outcome == 'failure' | |
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
| with: | |
| issue-number: ${{ github.event.issue.number }} | |
| body: | | |
| @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. | |
| See [CI log](https://github.com/genomic-medicine-sweden/nallo/actions/runs/${{ github.run_id }}) for more details. |