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Build and Test GATK 4

Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5987

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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] #5987

Triggered via pull request December 10, 2025 13:16
@mcovarrmcovarr
synchronize #9299
vs_1520_loftee
Status Success
Total duration 50m 0s
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
18m 9s
build and push gatk docker to artifacts
Validate script WDLs using womtools
2m 48s
Validate script WDLs using womtools
Validate generated WDLs using womtools
14m 28s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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8 errors
WDL test RUN_CNV_SOMATIC_WDL on cromwell
Process completed with exit code 1.
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The v0 series of google-github-actions/auth is no longer maintained.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
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The v0 series of google-github-actions/auth is no longer maintained.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
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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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
sha256:5c8b02ad2433bff8605a0168c63bcddcab00ff3b9d4df05e9228689a42424c6c
test-results-17.0.6+10-cloud
86.8 KB
sha256:e64e881f50ec94e58d25b7bfce0a8c40ce0ebae7481bc3c9fcb524196b5d3183
test-results-17.0.6+10-integration
577 KB
sha256:e6df8927dba4ea740ee34f3775e93b9225ec78282d32e26628fc70fdb100526c
test-results-17.0.6+10-unit
5.15 MB
sha256:6808ed41e8ff964ab862590e2307f1ede43b76bd145c46e27dd84b1732b8cfbd
test-results-docker-17.0.6+10-conda
59.6 KB
sha256:b4cd3dc0a5d2f32164895f7f71ec8e5e8360058a634f2906f8f9bf61be1384a3
test-results-docker-17.0.6+10-integration
580 KB
sha256:6e87dc1b970ebee62e3d2c472efc2d4248df414ff0698a9dd09e078fef3db33f
test-results-docker-17.0.6+10-unit
5.01 MB
sha256:50d946c0a186d2f2ff345a9708d5b5c72a99419fa848d3ca60e8bfd4ad92677b
test-results-docker-17.0.6+10-variantcalling
31.7 KB
sha256:bf4fa91fdc51a2581ca31decd95e6124c1aef9cd806d5eae9d27abf2dec815d3