Fixed a bug in pileup mode relating to number of haplotypes #2985
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; |