Swapped mito mode in Mutect to use the mode argument utils, providing… #1
nalinigansgatk-tests.yml
on: push
check if the environment has privileges
0s
build and push gatk docker to artifacts
17m 55s
Validate script WDLs using womtools
3m 54s
Validate generated WDLs using womtools
14m 21s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
22 warnings
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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/
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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.
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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/
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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/
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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.
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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/
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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/
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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.
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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, docker/build-push-action@v4, 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/
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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/
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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/
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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.
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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/
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WDL test RUN_CNV_GERMLINE_COHORT_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.
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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/
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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.
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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/
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Java 17.0.6+10 test on docker 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/download-artifact@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/
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Java 17.0.6+10 test on docker conda
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/download-artifact@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/
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Java 17.0.6+10 test on docker variantcalling
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/download-artifact@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/
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Java 17.0.6+10 test on docker 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/download-artifact@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/
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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: "gatkDockerImage", "test-results-17.0.6+10-integration", "test-results-17.0.6+10-unit", "test-results-docker-17.0.6+10-conda", "test-results-docker-17.0.6+10-integration", "test-results-docker-17.0.6+10-unit", "test-results-docker-17.0.6+10-variantcalling".
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/
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Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
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gatkDockerImage
Expired
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2.35 GB |
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test-results-17.0.6+10-integration
Expired
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3.5 MB |
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test-results-17.0.6+10-unit
Expired
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152 MB |
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test-results-docker-17.0.6+10-conda
Expired
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289 KB |
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test-results-docker-17.0.6+10-integration
Expired
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3.42 MB |
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test-results-docker-17.0.6+10-unit
Expired
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151 MB |
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test-results-docker-17.0.6+10-variantcalling
Expired
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243 KB |
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