Build and Test GATK 4

[DO NOT MERGE] #4945

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Triggered via pull request December 9, 2024 20:23

jamesemery

synchronize #9045

je_updateCondaEnvironment

Status Failure

Total duration 31m 51s

Artifacts 3

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

9 errors and 13 warnings

build and push gatk docker to artifacts

buildx failed with: ERROR: failed to solve: process "/bin/sh -c conda env create -vv -n gatk -f /gatk/gatkcondaenv.yml && echo \"source activate gatk\" >> /gatk/gatkenv.rc && echo \"source /gatk/gatk-completion.sh\" >> /gatk/gatkenv.rc && conda clean -afy && rm -rf /root/.cache/pip" did not complete successfully: 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.

WDL test RUN_CNV_SOMATIC_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_M2_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell

Process completed with exit code 1.

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The v0 series of google-github-actions/auth is no longer maintained.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

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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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

check if the environment has privileges

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

Validate script WDLs using womtools

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

build and push gatk docker to artifacts

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

WDL test RUN_CNV_SOMATIC_WDL on cromwell

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

WDL test RUN_M2_WDL on cromwell

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

Validate generated WDLs using womtools

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

Java 17.0.6+10 build and test unit

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

Java 17.0.6+10 build and test cloud

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

Java 17.0.6+10 build and test integration

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

Deprecation notice: v1, v2, and v3 of the artifact actions

The following artifacts were uploaded using a version of actions/upload-artifact that is scheduled for deprecation: "test-results-17.0.6+10-cloud", "test-results-17.0.6+10-integration", "test-results-17.0.6+10-unit". Please update your workflow to use v4 of the artifact actions. Learn more: https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions/

Artifacts

Produced during runtime

Name	Size
test-results-17.0.6+10-cloud	268 KB
test-results-17.0.6+10-integration	3.53 MB
test-results-17.0.6+10-unit	86.3 MB