Quarto notebooks #61
Workflow file for this run
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| #inspired by https://docs.cirro.bio/pipelines/development/#automated-testing | |
| name: Nextflow Tests | |
| on: | |
| pull_request: | |
| branches: | |
| - 'main' | |
| workflow_dispatch: | |
| jobs: | |
| unit-tests: | |
| name: Unit Tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| - name: Setup Java | |
| uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Install nf-test | |
| run: | | |
| wget -qO- https://get.nf-test.com | bash | |
| sudo mv nf-test /usr/local/bin | |
| - name: Run unit tests | |
| run: nf-test test tests/modules/ --verbose --junitxml=unit-test-results.xml | |
| - name: Publish unit test results | |
| if: always() | |
| uses: EnricoMi/publish-unit-test-result-action@v2 | |
| with: | |
| files: unit-test-results.xml | |
| check_name: Unit Test Results | |
| - name: Upload unit test results | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: unit-test-results | |
| path: | | |
| .nf-test/tests/ | |
| unit-test-results.xml | |
| pipeline-test: | |
| name: Pipeline Integration Test | |
| runs-on: ubuntu-latest | |
| needs: unit-tests | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| - name: Setup Java | |
| uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Install nf-test | |
| run: | | |
| wget -qO- https://get.nf-test.com | bash | |
| sudo mv nf-test /usr/local/bin | |
| - name: Run pipeline test | |
| run: nf-test test tests/main.nf.test --verbose --junitxml=pipeline-test-results.xml |