Build and Test GATK 4

Updated Python and PyMC, removed TensorFlow, and added PyTorch in conda environment. #3489

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Triggered via pull request December 8, 2023 00:40

samuelklee

synchronize #8561

sl_python_version_update

Status Failure

Total duration 1h 1m 54s

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

12 errors

WDL test RUN_CNN_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_CNV_SOMATIC_WDL on cromwell

Process completed with exit code 1.

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The v0 series of google-github-actions/auth is no longer maintained.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 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The v0 series of google-github-actions/auth is no longer maintained.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

WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell

Process completed with exit code 1.

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The v0 series of google-github-actions/auth is no longer maintained.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 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The v0 series of google-github-actions/auth is no longer maintained.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 conda

Process completed with exit code 1.

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The v0 series of google-github-actions/auth is no longer maintained.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 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The v0 series of google-github-actions/auth is no longer maintained.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 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

Artifacts

Produced during runtime

Name	Size
gatkDockerImage Expired	2.12 GB
test-results-17.0.6+10-cloud Expired	295 KB
test-results-17.0.6+10-integration Expired	3.57 MB
test-results-17.0.6+10-unit Expired	156 MB
test-results-docker-17.0.6+10-conda Expired	877 KB
test-results-docker-17.0.6+10-integration Expired	3.49 MB
test-results-docker-17.0.6+10-unit Expired	154 MB
test-results-docker-17.0.6+10-variantcalling Expired	234 KB