MarkDuplicates strategy of flow based reads that looks only at the qualities close to the end of the read #222
Workflow file for this run
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| # This is a github actions workflow which runs picard tests | |
| name: Build and Test | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| java: [ 17 ] | |
| experimental: [false] | |
| run_barclay_tests: [true, false] | |
| fail-fast: false | |
| continue-on-error: ${{ matrix.experimental }} | |
| name: Java ${{ matrix.Java }}, Barclay=${{ matrix.run_barclay_tests}} tests | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java ${{ matrix.Java }} | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: ${{ matrix.Java }} | |
| distribution: 'temurin' | |
| cache: gradle | |
| - name: "set up R" | |
| run: | | |
| wget -q -O - https://dl.google.com/linux/linux_signing_key.pub | sudo apt-key add - | |
| sudo apt-get -qq update | |
| sudo apt-get install -y --no-install-recommends r-base-dev r-recommended qpdf | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| - name: Compile with Gradle | |
| run: ./gradlew compileJava | |
| - name: Run tests | |
| run: | | |
| if [[ ${{matrix.run_barclay_tests}} == true ]]; then | |
| echo "Running tests using the Barclay command line parser." | |
| ./gradlew barclayTest | |
| else | |
| echo "Running tests using the legacy Picard command line parser." | |
| ./gradlew jacocoTestReport | |
| fi | |
| - name: "Build the jar and run a commandline test for sanity checking" | |
| run: | | |
| ./gradlew currentJar | |
| java -jar build/libs/picard.jar MarkDuplicates -I testdata/picard/sam/aligned_queryname_sorted.bam -O out.bam --METRICS_FILE out.metrics | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test-results-${{ matrix.Java }}-barclay-${{ matrix.run_barclay_tests}} | |
| path: build/reports/tests | |