Adding our nf-test tests to the GitHub Actions CI #3
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: nf-core template version comment | |
| # This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. | |
| # It posts a comment to the PR, even if it comes from a fork. | |
| on: pull_request_target | |
| jobs: | |
| template_version: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Read template version from .nf-core.yml | |
| uses: nichmor/minimal-read-yaml@v0.0.2 | |
| id: read_yml | |
| with: | |
| config: ${{ github.workspace }}/.nf-core.yml | |
| - name: Install nf-core | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} | |
| - name: Check nf-core outdated | |
| id: nf_core_outdated | |
| run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} | |
| - name: Post nf-core template version comment | |
| uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 | |
| if: | | |
| contains(env.OUTPUT, 'nf-core') | |
| with: | |
| repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} | |
| allow-repeats: false | |
| message: | | |
| > [!WARNING] | |
| > Newer version of the nf-core template is available. | |
| > | |
| > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. | |
| > Please update your pipeline to the latest version. | |
| > | |
| > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). | |
| # |