VS-1327 ensure sample ids are unique echo callset version #4151
gbggrantgatk-tests.yml
on: pull_request
check if the environment has privileges
0s
build and push gatk docker to artifacts
29m 42s
Validate script WDLs using womtools
1m 45s
Validate generated WDLs using womtools
13m 56s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
14 errors and 23 warnings
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Java 17.0.6+10 build and test unit
The v0 series of google-github-actions/setup-gcloud is no longer maintained.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/setup-gcloud
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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The v0 series of google-github-actions/auth is no longer maintained.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
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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The v0 series of google-github-actions/auth is no longer maintained.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
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Java 17.0.6+10 build and test cloud
The v0 series of google-github-actions/setup-gcloud is no longer maintained.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/setup-gcloud
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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The v0 series of google-github-actions/auth is no longer maintained.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
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Java 17.0.6+10 build and test integration
The v0 series of google-github-actions/setup-gcloud is no longer maintained.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/setup-gcloud
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Java 17.0.6+10 test on docker unit
The v0 series of google-github-actions/setup-gcloud is no longer maintained.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/setup-gcloud
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Java 17.0.6+10 test on docker 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
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Java 17.0.6+10 test on docker conda
The v0 series of google-github-actions/setup-gcloud 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/setup-gcloud
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Java 17.0.6+10 test on docker conda
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
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Java 17.0.6+10 test on docker variantcalling
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
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Java 17.0.6+10 test on docker variantcalling
The v0 series of google-github-actions/setup-gcloud 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/setup-gcloud
|
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Java 17.0.6+10 test on docker 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
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Java 17.0.6+10 test on docker integration
The v0 series of google-github-actions/setup-gcloud 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/setup-gcloud
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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/.
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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/.
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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/.
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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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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/.
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WDL test RUN_CNN_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 unit
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, google-github-actions/setup-gcloud@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/.
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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/.
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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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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, google-github-actions/setup-gcloud@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/.
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WDL test RUN_CNV_GERMLINE_COHORT_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/.
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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_SOMATIC_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/.
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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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build and push gatk docker to artifacts
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, docker/metadata-action@v4, docker/setup-buildx-action@v2, docker/build-push-action@v4, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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WDL test RUN_CNV_GERMLINE_CASE_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/.
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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
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, google-github-actions/setup-gcloud@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/.
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Java 17.0.6+10 test on docker unit
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, google-github-actions/setup-gcloud@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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Java 17.0.6+10 test on docker conda
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, google-github-actions/setup-gcloud@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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Java 17.0.6+10 test on docker variantcalling
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, google-github-actions/setup-gcloud@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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Java 17.0.6+10 test on docker integration
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, google-github-actions/setup-gcloud@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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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-cloud", "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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2.32 GB |
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test-results-17.0.6+10-cloud
Expired
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333 KB |
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test-results-17.0.6+10-integration
Expired
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3.45 MB |
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test-results-17.0.6+10-unit
Expired
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157 MB |
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test-results-docker-17.0.6+10-conda
Expired
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281 KB |
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test-results-docker-17.0.6+10-integration
Expired
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3.37 MB |
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test-results-docker-17.0.6+10-unit
Expired
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155 MB |
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test-results-docker-17.0.6+10-variantcalling
Expired
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232 KB |
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