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(Do not merge) Port of nvscorevariants into GATK, with a basic tool frontend #4677

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(Do not merge) Port of nvscorevariants into GATK, with a basic tool frontend

(Do not merge) Port of nvscorevariants into GATK, with a basic tool frontend #4677

Triggered via pull request September 27, 2024 20:38
@droazendroazen
synchronize #8004
dr_nvscorevariants
Status Failure
Total duration 29m 37s
Artifacts 3

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
21s
build and push gatk docker to artifacts
Validate script WDLs using womtools
4m 1s
Validate script WDLs using womtools
Validate generated WDLs using womtools
14m 47s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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5 errors and 16 warnings
build and push gatk docker to artifacts
The process '/usr/bin/docker' failed 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The v0 series of google-github-actions/auth is no longer maintained.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
WDL test RUN_CNV_GERMLINE_COHORT_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The v0 series of google-github-actions/auth is no longer maintained.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 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The v0 series of google-github-actions/auth is no longer maintained.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
build and push gatk docker to artifacts
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, docker/metadata-action@v4, docker/setup-buildx-action@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Validate script WDLs using womtools
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
Validate generated WDLs using womtools
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
WDL test RUN_M2_WDL on cromwell
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
WDL test RUN_M2_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
Java 17.0.6+10 build and test unit
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
WDL test RUN_CNV_SOMATIC_WDL on cromwell
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
WDL test RUN_CNV_SOMATIC_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
Java 17.0.6+10 build and test cloud
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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/
Java 17.0.6+10 build and test integration
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Artifacts

Produced during runtime
Name Size
test-results-17.0.6+10-cloud
302 KB
test-results-17.0.6+10-integration
3.5 MB
test-results-17.0.6+10-unit
152 MB