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Build and Test GATK 4

Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5979

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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] #5979

Triggered via pull request December 9, 2025 10:47
@mcovarrmcovarr
synchronize #9299
vs_1520_loftee
Status Success
Total duration 44m 43s
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 14s
build and push gatk docker to artifacts
Validate script WDLs using womtools
2m 52s
Validate script WDLs using womtools
Validate generated WDLs using womtools
14m 38s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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8 errors
WDL test RUN_CNV_GERMLINE_CASE_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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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
sha256:268c50f879d9f95ff0e896670aa81a50930362af7f07b0d8330441c81c8866ac
test-results-17.0.6+10-cloud
86.8 KB
sha256:f108c9e8c44d12b7dc1957b9dfe85574a4a8af0f86c6d03c48caf156012d46a6
test-results-17.0.6+10-integration
577 KB
sha256:89b162779f22eafc762ddbea9c090c44b6921a616d54c7cb0c4a7f8dbd03f886
test-results-17.0.6+10-unit
5.14 MB
sha256:bd54b358a015a803083e8d57fb85c9dc9d5cc2600b2ebf4878a7ac7aef885380
test-results-docker-17.0.6+10-conda
59.5 KB
sha256:8c66826e22ac02ac77c2b32237e4675165a3088019d83853f30c8c88b66e2ae5
test-results-docker-17.0.6+10-integration
579 KB
sha256:e42bcf57c13f13f54f02f67055408fbfe3bf7aa69780fab5805c0d1c1c39d532
test-results-docker-17.0.6+10-unit
5.01 MB
sha256:2ee52920de520d0bde4ccf25b74c35f6c62c3076bda119e75cd25148bef24932
test-results-docker-17.0.6+10-variantcalling
31.9 KB
sha256:d9a6fe13ab69c81e0a12c5f6734a9e71ed5ae8bb8e1d5d88c400820a6e297924