add basic GitHub action testing #18
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: Nextflow Stub Run | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ '**' ] | |
| jobs: | |
| stub-run: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| config: [ | |
| 'test-diann.config', | |
| 'test-encyclopedia-narrow-gpf.config', | |
| 'test-encyclopedia-wide-only.config' | |
| ] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Run (${{ matrix.config }}) | |
| run: | | |
| echo "Installing Nextflow:" | |
| curl -s https://get.nextflow.io | bash | |
| chmod +x nextflow | |
| echo "Running Nextflow stub with config: ${{ matrix.config }}" | |
| ./nextflow secrets set PANORAMA_API_KEY "PLACEHOLDER" | |
| ./nextflow run . -stub-run -c test-resources/${{ matrix.config }} |