MarkDuplicates strategy of flow based reads that looks only at the qualities close to the end of the read #128
Workflow file for this run
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| name: Cloud Tests | |
| on: | |
| push: | |
| branches: | |
| - 'master' | |
| pull_request: | |
| workflow_dispatch: | |
| env: | |
| PICARD_TEST_INPUTS: gs://hellbender/test/resources/ | |
| PICARD_TEST_STAGING: gs://hellbender-test-logs/staging/ | |
| PICARD_TEST_LOGS: /hellbender-test-logs/build_reports/ | |
| PICARD_TEST_PROJECT: broad-dsde-dev | |
| jobs: | |
| ## This workaround is necessary since there is no equivalent to the old TRAVIS_SECURE_ENVIRONMENT variable that indicated | |
| ## if a run was privileged and had secrets. Since the GCP credentials are necessary for all tests in order to upload their, | |
| ## results that makes them a reasonable proxy for testing the credentials of this entire execution. https://github.com/actions/runner/issues/520 | |
| check-secrets: | |
| name: check if the environment has privileges | |
| outputs: | |
| google-credentials: ${{ steps.google-credentials.outputs.defined }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: google-credentials | |
| env: | |
| GCP_CREDENTIALS: ${{ secrets.GCP_CREDENTIALS }} | |
| if: "${{ env.GCP_CREDENTIALS != '' }}" | |
| run: echo defined=true >> $GITHUB_OUTPUT | |
| test: | |
| runs-on: ubuntu-latest | |
| needs: check-secrets | |
| strategy: | |
| matrix: | |
| java: [ 17 ] | |
| run_barclay_tests: [true, false] | |
| experimental: [ false ] | |
| fail-fast: false | |
| continue-on-error: ${{ matrix.experimental }} | |
| name: Java ${{ matrix.Java }}, Barclay=${{ matrix.run_barclay_tests}} cloud tests | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: 'Set up java ${{ matrix.Java }}' | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: ${{ matrix.Java }} | |
| distribution: 'temurin' | |
| cache: gradle | |
| - name: 'Compile with Gradle' | |
| run: | | |
| ./gradlew compileJava | |
| ./gradlew installDist | |
| #Google Cloud stuff | |
| - id: 'gcloud-auth' | |
| if: needs.check-secrets.outputs.google-credentials == 'true' | |
| uses: google-github-actions/auth@v0 | |
| with: | |
| credentials_json: ${{ secrets.GCP_CREDENTIALS }} | |
| project_id: ${{ env.PICARD_TEST_PROJECT }} | |
| create_credentials_file: true | |
| - name: 'Set up Cloud SDK' | |
| if: needs.check-secrets.outputs.google-credentials == 'true' | |
| uses: google-github-actions/setup-gcloud@v2 | |
| - name: compile test code | |
| if: needs.check-secrets.outputs.google-credentials == 'true' | |
| run: ./gradlew compileTestJava | |
| - name: Run tests | |
| if: needs.check-secrets.outputs.google-credentials == 'true' | |
| env: | |
| TEST_TYPE: cloud | |
| run: | | |
| if [[ ${{matrix.run_barclay_tests}} == true ]]; then | |
| echo "Running tests using the Barclay command line parser." | |
| ./gradlew barclayTest | |
| else | |
| echo "Running tests using the legacy Picard command line parser." | |
| ./gradlew jacocoTestReport | |
| fi | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: cloud-test-results-${{ matrix.Java }}-barclay-${{ matrix.run_barclay_tests}} | |
| path: build/reports/tests |