feat: FastqToBam can extract UMI(s) from the comment in the read name #1179
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| name: unit tests | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| environment: github-actions | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Setup Scala | |
| uses: olafurpg/setup-scala@v12 | |
| with: | |
| java-version: adopt-openj9@1.8.0-292 | |
| - name: Unit Tests | |
| run: | | |
| set -e | |
| sbt +clean coverage +test && sbt coverageReport coverageAggregate && (find $HOME/.sbt -name "*.lock" | xargs rm) && (find $HOME/.ivy2 -name "ivydata-*.properties" | xargs rm) | |
| - name: Code Coverage | |
| uses: codecov/codecov-action@v3.1.0 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| flags: unittests # optional | |
| fail_ci_if_error: true # optional (default = false) | |
| verbose: true # optional (default = false) | |
| - name: Cache .ivy2 | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/.ivy2 | |
| key: ${{ runner.os }}-ivy2-${{ hashFiles('**/build.sbt') }} | |
| - name: Cache .sbt | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/.sbt | |
| key: ${{ runner.os }}-sbt-${{ hashFiles('**/build.properties') }} | |
| release: | |
| if: github.repository == 'fulcrumgenomics/fgbio' && github.ref == 'refs/heads/main' | |
| needs: test | |
| runs-on: ubuntu-latest | |
| env: | |
| SONATYPE_USER: ${{ secrets.SONATYPE_USER }} | |
| SONATYPE_PASS: ${{ secrets.SONATYPE_PASS }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup Scala | |
| uses: olafurpg/setup-scala@v12 | |
| with: | |
| java-version: adopt-openj9@1.8.0-292 | |
| - name: Upload to Sonatype | |
| run: | | |
| sbt +publish |