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Port of nvscorevariants into GATK, with a basic tool frontend #4676

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Port of nvscorevariants into GATK, with a basic tool frontend

Port of nvscorevariants into GATK, with a basic tool frontend #4676

Triggered via pull request September 27, 2024 20:33
@droazendroazen
synchronize #8004
dr_nvscorevariants
Status Failure
Total duration 3m 9s
Artifacts –

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
17s
build and push gatk docker to artifacts
Validate script WDLs using womtools
1m 6s
Validate script WDLs using womtools
Validate generated WDLs using womtools
1m 5s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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14 errors and 14 warnings
build and push gatk docker to artifacts
The process '/usr/bin/docker' failed with exit code 1
Validate generated WDLs using womtools
Process completed with exit code 1.
Validate script WDLs using womtools
Process completed with exit code 1.
Java 17.0.6+10 build and test integration
Process completed with exit code 1.
Java 17.0.6+10 build and test integration
Process completed with exit code 1.
Java 17.0.6+10 build and test cloud
Process completed with exit code 1.
Java 17.0.6+10 build and test cloud
Process completed with exit code 1.
Java 17.0.6+10 build and test unit
Process completed with exit code 1.
Java 17.0.6+10 build and test unit
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_GERMLINE_COHORT_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_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
Process completed with exit code 1.
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 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/
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/
Java 17.0.6+10 build and test integration
No files were found with the provided path: build/reports/tests. No artifacts will be uploaded.
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, 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/
Java 17.0.6+10 build and test cloud
No files were found with the provided path: build/reports/tests. No artifacts will be uploaded.
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, 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/
Java 17.0.6+10 build and test unit
No files were found with the provided path: build/reports/tests. No artifacts will be uploaded.
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, 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_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_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_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_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/