force CI writability #12
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| name: Nextflow Test Pipeline Conda | |
| on: | |
| push: | |
| branches: [ main, dev ] | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| - name: Setup Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: 3.9 | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: strict | |
| - name: Install Nextflow | |
| run: | | |
| curl -s https://get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| nextflow -version | |
| - name: Run Nextflow pipeline | |
| run: | | |
| nextflow run main.nf -profile test -with-conda | |
| - name: Check test completion and details | |
| run: | | |
| # Check if the test.passed file was created | |
| if [ ! -f "results/test/test.passed" ]; then | |
| echo "ERROR: Test completion file 'results/test/test.passed' not found" | |
| echo "Test pipeline did not complete successfully" | |
| exit 1 | |
| fi | |
| echo "✅ Test completed successfully!" | |
| - name: Upload test results | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: nextflow-test-results | |
| path: | | |
| results/ | |
| .nextflow.log | |
| retention-days: 7 |