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Build and Test GATK 4

Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5981

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Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767]

Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5981

Triggered via pull request December 9, 2025 11:36
@mcovarrmcovarr
synchronize #9299
vs_1520_loftee
Status Success
Total duration 45m 21s
Artifacts 8

gatk-tests.yml

on: pull_request
check if the environment has privileges
3s
check if the environment has privileges
build and push gatk docker to artifacts
13m 16s
build and push gatk docker to artifacts
Validate script WDLs using womtools
2m 54s
Validate script WDLs using womtools
Validate generated WDLs using womtools
14m 45s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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10 errors
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
Process completed with exit code 1.
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
Process completed with exit code 1.
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
Process completed with exit code 1.
unit build and test Java 17.0.6+10
The v0 series of google-github-actions/auth is no longer maintained.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
cloud build and test Java 17.0.6+10
The v0 series of google-github-actions/auth is no longer maintained.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
integration build and test Java 17.0.6+10
The v0 series of google-github-actions/auth is no longer maintained.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
unit test on docker Java 17.0.6+10
The v0 series of google-github-actions/auth is no longer maintained.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
conda test on docker Java 17.0.6+10
The v0 series of google-github-actions/auth is no longer maintained.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
variantcalling test on docker Java 17.0.6+10
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
integration test on docker Java 17.0.6+10
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

Artifacts

Produced during runtime
Name Size Digest
gatkDockerImage
2.29 GB
sha256:9d3846d9b6dcd4a49f50c777e2f21179e4694e22aef4bb724d9143dd5bcff365
test-results-17.0.6+10-cloud
86.9 KB
sha256:f45dbfb192ca701c553e9a39f4bbb20ed28a0ff587033955559960a759f996c8
test-results-17.0.6+10-integration
578 KB
sha256:676997b827cb3bed354f919cbf2ebd8151096329919574279c3d5ad3f8220e46
test-results-17.0.6+10-unit
5.15 MB
sha256:c368ec6e7677a13901848ac3bb3648473c793ccd91be15533a0ccbd5ae4202e9
test-results-docker-17.0.6+10-conda
59.4 KB
sha256:39a0c0efd369f39ac2635247ce36f233e7efaadcce8bd3eb4a510bfd4a42664e
test-results-docker-17.0.6+10-integration
580 KB
sha256:49f2305f293a1ae616f2fa1e53281ce5b4a5eb3c58bf5bb3657017195d2f1947
test-results-docker-17.0.6+10-unit
5.01 MB
sha256:b96dcff303f069e6a64badfdff63a1afa0d2a3d16b342a3b2818e5233e169951
test-results-docker-17.0.6+10-variantcalling
31.8 KB
sha256:e1c8c12761385c14f11a2d83d1cc8901d352eba4547153f6bd66f24116199846