Merge dev to master #14
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 CI | |
| on: | |
| push: | |
| branches: | |
| - development | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| test_sarscov2_user: | |
| name: Run pipeline test (user) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline test (user) | |
| run: | | |
| nextflow run main.nf -profile docker --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml | |
| test_sarscov2_reference: | |
| name: Run pipeline test (reference) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline test (reference) | |
| run: | | |
| nextflow run main.nf -profile docker --prefix "covidmvp-$(date +%Y-%m-%d)" --end_date $(date +%Y-%m-%d) -params-file covidmvp_clinical_params.yaml | |
| check_success: | |
| name: Check if all tests passed | |
| needs: [test_sarscov2_user, test_sarscov2_reference] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check job status | |
| if: ${{ failure() }} | |
| run: exit 1 |