Changed flow allele filtering in Mutect2 to work separately on the tumor and the normal samples #3
Workflow file for this run
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| name: Test GATK 4 only tests, no WDL | |
| concurrency: | |
| group: gatk-tests-ci-${{ github.ref }} | |
| cancel-in-progress: true | |
| on: | |
| push: | |
| branches: | |
| - 'master' | |
| pull_request: | |
| workflow_dispatch: | |
| inputs: | |
| branch: | |
| description: 'Branch to run workflow on' | |
| required: true | |
| default: 'master' | |
| env: | |
| TERM: dumb | |
| GRADLE_OPTS: "-Xmx2048m -Dorg.gradle.daemon=false" | |
| HELLBENDER_TEST_INPUTS: gs://hellbender/test/resources/ | |
| HELLBENDER_TEST_STAGING: gs://hellbender-test-logs/staging/ | |
| HELLBENDER_TEST_LOGS: /hellbender-test-logs/build_reports/ | |
| HELLBENDER_TEST_PROJECT: broad-dsde-dev | |
| TEST_VERBOSITY: minimal | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| 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 | |
| #Run our non-docker tests | |
| test: | |
| runs-on: ubuntu-latest | |
| needs: check-secrets | |
| strategy: | |
| matrix: | |
| java: [ 17.0.6+10 ] | |
| experimental: [ false ] | |
| scalaVersion: [ 2.13 ] | |
| testType: [ integration, unit, variantcalling ] | |
| fail-fast: false | |
| continue-on-error: ${{ matrix.experimental }} | |
| env: | |
| TEST_TYPE: ${{ matrix.testType }} | |
| SCALA_VERSION: ${{ matrix.scalaVersion }} | |
| name: Java ${{ matrix.Java }} build and test ${{ matrix.testType }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| ref: ${{ github.event.inputs.branch || github.ref }} | |
| - uses: ./.github/actions/purge-runner-disk | |
| - 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: ${{ env.HELLBENDER_TEST_PROJECT }} | |
| create_credentials_file: true | |
| - name: "export the credentials for GATK tests" | |
| if: needs.check-secrets.outputs.google-credentials == 'true' | |
| run: echo "HELLBENDER_JSON_SERVICE_ACCOUNT_KEY=${{ steps.auth.outputs.credentials_file_path }}" >> $GITHUB_ENV | |
| - name: 'Set up Cloud SDK' | |
| if: needs.check-secrets.outputs.google-credentials == 'true' | |
| uses: google-github-actions/setup-gcloud@v2 | |
| - name: pull lfs files | |
| run: git lfs pull | |
| - name: compile test code | |
| run: ./gradlew compileTestJava | |
| - name: run-tests | |
| if: ${{ needs.check-secrets.outputs.google-credentials == 'true' || matrix.testType != 'cloud'}} | |
| id: jacoco-tests | |
| run: | | |
| ./gradlew --daemon -Dscala.version=${{ env.SCALA_VERSION }} jacocoTestReport | |
| - uses: ./.github/actions/upload-gatk-test-results | |
| if: always() | |
| with: | |
| warnPR: ${{ github.event_name == 'pull_request' && steps.jacoco-tests.outcome != 'success' }} | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| job-matrix-id: ${{ github.run_id }}.1${{ strategy.job-index }} | |
| repo-path: ${{ github.ref_name }}_${{ github.run_id }}.1${{ strategy.job-index }} | |
| bot-comment-key: ${{ secrets.GATK_BOT_COMMENT_KEY }} | |
| identifier: Java ${{ matrix.Java }} build and test ${{ matrix.testType }} | |
| only-artifact: ${{ needs.check-secrets.outputs.google-credentials != 'true' }} | |