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Tool to detect CRAM base corruption caused by GATK issue 8768 #4177

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Tool to detect CRAM base corruption caused by GATK issue 8768

Tool to detect CRAM base corruption caused by GATK issue 8768 #4177

Triggered via pull request May 13, 2024 15:27
@cmnbroadcmnbroad
synchronize #8819
cn_cram_fix
Status Cancelled
Total duration 20m 40s
Artifacts 2

gatk-tests.yml

on: pull_request
check if the environment has privileges
0s
check if the environment has privileges
build and push gatk docker to artifacts
19m 53s
build and push gatk docker to artifacts
Validate script WDLs using womtools
58s
Validate script WDLs using womtools
Validate generated WDLs using womtools
13m 45s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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15 errors and 7 warnings
Java 17.0.6+10 build and test cloud
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The v0 series of google-github-actions/auth is no longer maintained.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
build and push gatk docker to artifacts
The run was canceled by @cmnbroad.
build and push gatk docker to artifacts
The operation was canceled.
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
The run was canceled by @cmnbroad.
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
The operation was canceled.
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
The run was canceled by @cmnbroad.
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
The operation was canceled.
WDL test RUN_CNV_SOMATIC_WDL on cromwell
The run was canceled by @cmnbroad.
WDL test RUN_CNV_SOMATIC_WDL on cromwell
The operation was canceled.
Java 17.0.6+10 build and test integration
The run was canceled by @cmnbroad.
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The v0 series of google-github-actions/auth is no longer maintained.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 build and test integration
The operation was canceled.
Java 17.0.6+10 build and test unit
The run was canceled by @cmnbroad.
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The v0 series of google-github-actions/auth is no longer maintained.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
Validate script WDLs using womtools
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Validate generated WDLs using womtools
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Java 17.0.6+10 build and test cloud
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
WDL test RUN_CNN_WDL on cromwell
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
WDL test RUN_M2_WDL on cromwell
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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-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 Expired
279 KB
test-results-17.0.6+10-unit Expired
152 MB