Build and Test GATK 4

Fix the Spark version in the GATK jar manifest, and use the right constant in build.gradle #3570

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Triggered via pull request December 13, 2023 21:23

droazen

opened #8625

dr_update_spark_version_in_manifest

Status Success

Total duration 57m 31s

Artifacts 8

gatk-tests.yml

on: pull_request

check if the environment has privileges

build and push gatk docker to artifacts

Validate script WDLs using womtools

Validate generated WDLs using womtools

Matrix: wdlTests

Matrix: test

Matrix: testOnDocker

Annotations

14 errors and 5 warnings

Java 17.0.6+10 build and test cloud

The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/auth

Java 17.0.6+10 build and test cloud

The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/setup-gcloud

Java 17.0.6+10 build and test unit

The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/setup-gcloud

Java 17.0.6+10 build and test unit

The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/auth

Java 17.0.6+10 build and test integration

The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/auth

Java 17.0.6+10 build and test integration

The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/setup-gcloud

Java 17.0.6+10 test on docker unit

The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/setup-gcloud

Java 17.0.6+10 test on docker unit

The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/auth

Java 17.0.6+10 test on docker variantcalling

The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/auth

Java 17.0.6+10 test on docker variantcalling

The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/setup-gcloud

Java 17.0.6+10 test on docker conda

The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/setup-gcloud

Java 17.0.6+10 test on docker conda

The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/auth

Java 17.0.6+10 test on docker integration

The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/auth

Java 17.0.6+10 test on docker integration

The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/setup-gcloud

WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell

Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.

WDL test RUN_CNN_WDL on cromwell

Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.

WDL test RUN_M2_WDL on cromwell

Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.

WDL test RUN_CNV_SOMATIC_WDL on cromwell

Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.

WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell

Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.

Artifacts

Produced during runtime

Name	Size
gatkDockerImage Expired	2.31 GB
test-results-17.0.6+10-cloud Expired	294 KB
test-results-17.0.6+10-integration Expired	3.57 MB
test-results-17.0.6+10-unit Expired	152 MB
test-results-docker-17.0.6+10-conda Expired	316 KB
test-results-docker-17.0.6+10-integration Expired	3.5 MB
test-results-docker-17.0.6+10-unit Expired	151 MB
test-results-docker-17.0.6+10-variantcalling Expired	241 KB