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Build and Test GATK 4

Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5985

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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] #5985

Triggered via pull request December 9, 2025 21:44
@mcovarrmcovarr
synchronize #9299
vs_1520_loftee
Status Success
Total duration 48m 33s
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 46s
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 50s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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9 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.
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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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
sha256:4caf10b08c3901eb751fa5087e7ab9444e53ccd7b96c3a3ed48b13dbf02961aa
test-results-17.0.6+10-cloud
86.9 KB
sha256:0446143ee475b61d2effbbd7ef061eea55fe5b5f0c6d3671b622b5dca7a8629c
test-results-17.0.6+10-integration
577 KB
sha256:88e760cf63650cddb377389810f1d8613e01dd5576873eb4650007492a184b01
test-results-17.0.6+10-unit
5.15 MB
sha256:f341db76a839ea452a5f6bf01caf8e068121fbdfc6b53f6f71f5a753225155c8
test-results-docker-17.0.6+10-conda
59.5 KB
sha256:7979ee1878c5ecbef52fb7d8534e709fc85bb8d493bb0da431ab814bb3b16286
test-results-docker-17.0.6+10-integration
580 KB
sha256:8464fedc1d7ed3e345e62cb453bc9c43e4b54c742f75317e29655767149018ed
test-results-docker-17.0.6+10-unit
5 MB
sha256:1da2909329c206f0896ea0f001cd6ca749040dd9b55b09122dfb20746f39f658
test-results-docker-17.0.6+10-variantcalling
31.8 KB
sha256:1402007560ad10db0843646f69791a0079cddd2a39d3df5bdf095d0065599fe5