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VS 1528 Update the sharding of the samples in the VAT creation to be dependent on the number of samples #4877

VS 1528 Update the sharding of the samples in the VAT creation to be dependent on the number of samples

VS 1528 Update the sharding of the samples in the VAT creation to be dependent on the number of samples #4877

Workflow file for this run

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;