Add TemplateCoordinate sort order to the usage of SortBam #1185
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |