Add a native GATK implementation for 2bit references, and remove the dependency on the ADAM library #3505
Workflow file for this run
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| name: Build and Test GATK 4 | |
| on: | |
| push: | |
| branches: | |
| - 'master' | |
| pull_request: | |
| workflow_dispatch: | |
| env: | |
| CROMWELL_VERSION: 84 | |
| 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 | |
| buildDocker: | |
| name: build and push gatk docker to artifacts | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout gatk | |
| uses: actions/checkout@v3 | |
| - uses: ./.github/actions/purge-runner-disk | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| tags: | | |
| type=raw,value=${{github.sha}} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@v4 | |
| with: | |
| context: . | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| outputs: type=docker,dest=/tmp/myimage.tar | |
| # By uploading the docker image as an artifact we save ourselves the requirement for the image to be built with ghcr push permission | |
| - name: Upload docker image as artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: gatkDockerImage | |
| path: /tmp/myimage.tar | |
| #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: [ cloud, integration, unit ] | |
| 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 | |
| - 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@v0 | |
| - 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' }} | |
| #Run our docker tests | |
| testOnDocker: | |
| needs: [buildDocker, check-secrets] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| java: [ 17.0.6+10 ] | |
| experimental: [ false ] | |
| scalaVersion: [ 2.13 ] | |
| testType: [ integration, unit, variantcalling, conda ] | |
| fail-fast: false | |
| continue-on-error: ${{ matrix.experimental }} | |
| env: | |
| TEST_TYPE: ${{ matrix.testType }} | |
| SCALA_VERSION: ${{ matrix.scalaVersion }} | |
| name: Java ${{ matrix.Java }} test on docker ${{matrix.testType}} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 #TODO make this shallow | |
| - 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 | |
| #Google Cloud stuff | |
| - id: 'gcloud-auth' | |
| uses: google-github-actions/auth@v0 | |
| if: needs.check-secrets.outputs.google-credentials == 'true' | |
| 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@v0 | |
| - name: build test jars | |
| run: ./gradlew clean shadowTestClassJar shadowTestJar | |
| - name: set up test folders and links | |
| run: | | |
| mkdir ./testJars; | |
| echo $( find ./build/libs/ -name "gatk*test.jar"); | |
| cp -r $( find ./build/libs/ -name "gatk*test.jar" ) ./testJars; | |
| cp -r $( find ./build/libs/ -name "gatk*testDependencies.jar" ) ./testJars; | |
| mkdir -p build/reports/; | |
| chmod -R a+w build/reports/; | |
| cp scripts/docker/dockertest.gradle . | |
| - name: Download docker image artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: gatkDockerImage | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/myimage.tar | |
| docker image ls -a | |
| - name: pull lfs files | |
| run: git lfs pull | |
| - name: run-docker-tests | |
| id: docker-jacocco-tests | |
| run: | | |
| docker run \ | |
| -v $(pwd):/gatkCloneMountPoint:cached \ | |
| -v $(pwd)/testJars:/jars:cached \ | |
| --rm \ | |
| -e "scala.version=${SCALA_VERSION}" \ | |
| -e "TEST_VERBOSITY=minimal" \ | |
| -e "TEST_TYPE=${TEST_TYPE}" \ | |
| -t ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.sha }} \ | |
| bash --init-file /gatk/gatkenv.rc /root/run_unit_tests.sh; | |
| TEST_EXIT_VALUE=$?; | |
| $( exit ${TEST_EXIT_VALUE} ); | |
| sudo chmod -R a+w build/reports/; | |
| mkdir build/reports/tests/test \ | |
| && cp -rp build/reports/tests/testOnPackagedReleaseJar/* build/reports/tests/test \ | |
| && rm -r build/reports/tests/testOnPackagedReleaseJar; | |
| - uses: ./.github/actions/upload-gatk-test-results | |
| if: always() | |
| with: | |
| warnPR: ${{ github.event_name == 'pull_request' && steps.docker-jacocco-tests.outcome != 'success' }} | |
| is-docker: true | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| job-matrix-id: ${{ github.run_id }}.${{ strategy.job-index }} | |
| repo-path: ${{ github.ref_name }}_${{ github.run_id }}.${{ strategy.job-index }} | |
| bot-comment-key: ${{ secrets.GATK_BOT_COMMENT_KEY }} | |
| identifier: Java ${{ matrix.Java }} test on docker ${{matrix.testType}} | |
| only-artifact: ${{ needs.check-secrets.outputs.google-credentials != 'true' }} | |
| #run wdl validation on WDLs in the scripts directory | |
| scriptsWdlValidation: | |
| runs-on: ubuntu-latest | |
| name: Validate script WDLs using womtools | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: ./.github/actions/purge-runner-disk | |
| - name: Set up java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'temurin' | |
| cache: gradle | |
| - uses: ./.github/actions/install-cromwell | |
| with: | |
| CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }} | |
| - name: Run Scripts WDL Validation Test | |
| run: ./gradlew gatkValidateScriptsWdl | |
| #run wdl validation on generated WDLs | |
| generatedWdlValidation: | |
| runs-on: ubuntu-latest | |
| name: Validate generated WDLs using womtools | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: ./.github/actions/purge-runner-disk | |
| - name: Set up java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'temurin' | |
| cache: gradle | |
| - uses: ./.github/actions/install-cromwell | |
| with: | |
| CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }} | |
| - name: Run Generated WDL Validation Test | |
| run: ./gradlew gatkValidateGeneratedWdl | |
| #Run our various targeted medium scale wdl wiring tests | |
| wdlTests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| wdlTest: [ 'RUN_CNV_GERMLINE_COHORT_WDL', 'RUN_CNV_GERMLINE_CASE_WDL', 'RUN_CNV_SOMATIC_WDL', 'RUN_M2_WDL', 'RUN_CNN_WDL', 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' ] | |
| continue-on-error: true | |
| name: WDL test ${{ matrix.wdlTest }} on cromwell | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: ./.github/actions/purge-runner-disk | |
| - name: pull lfs files | |
| run: git lfs pull | |
| - name: Set up java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'temurin' | |
| cache: gradle | |
| - uses: ./.github/actions/install-cromwell | |
| with: | |
| CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }} | |
| - name: "Exporting Environment Variables for Wdl Scripts" | |
| run: | | |
| if [[ "${{ github.event_name }}" == "pull_request" ]] | |
| then | |
| echo "CI_PULL_REQUEST=${{ github.event.number }}" >> $GITHUB_ENV | |
| fi | |
| echo "CI_COMMIT=${{ github.sha }}" >> $GITHUB_ENV | |
| - name: "CNV_GERMLINE_COHORT_WDL_TEST" | |
| if: ${{ matrix.wdlTest == 'RUN_CNV_GERMLINE_COHORT_WDL' }} | |
| run: | | |
| echo "Running CNV germline cohort workflow"; | |
| bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh COHORT; | |
| - name: "CNV_GERMLINE_CASE_WDL_TEST" | |
| if: ${{ matrix.wdlTest == 'RUN_CNV_GERMLINE_CASE_WDL' }} | |
| run: | | |
| echo "Running CNV germline case workflow"; | |
| bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh CASE; | |
| - name: "CNV_SOMATIC_WDL_TEST" | |
| if: ${{ matrix.wdlTest == 'RUN_CNV_SOMATIC_WDL' }} | |
| run: | | |
| echo "Running CNV somatic workflows"; | |
| bash scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh; | |
| - name: "M2_WDL_TEST" | |
| if: ${{ matrix.wdlTest == 'RUN_M2_WDL' }} | |
| run: | | |
| echo "Deleting some unused files before running M2 WDL..."; | |
| rm -Rf src/test/resources/large/VQSR; | |
| echo "Running M2 WDL"; | |
| bash scripts/m2_cromwell_tests/run_m2_wdl.sh; | |
| - name: "CNN_WDL_TEST" | |
| if: ${{ matrix.wdlTest == 'RUN_CNN_WDL' }} | |
| run: | | |
| echo "Running CNN WDL"; | |
| bash scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh; | |
| - name: "VCF_SITE_LEVEL_FILTERING_WDL_TEST" | |
| if: ${{ matrix.wdlTest == 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' }} | |
| run: | | |
| echo "Running VCF Site Level Filtering WDL"; | |
| bash scripts/vcf_site_level_filtering_cromwell_tests/run_vcf_site_level_filtering_wdl.sh; |