VS-1490 - Refactor python code from extract dir into a scripts directory. #4880
Triggered via pull request
November 13, 2024 22:18
gbggrant
Status
Success
Total duration
2h 59m 10s
Artifacts
8
gatk-tests.yml
on: pull_request
check if the environment has privileges
0s
build and push gatk docker to artifacts
2h 20m
Validate script WDLs using womtools
57s
Validate generated WDLs using womtools
13m 22s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
20 errors and 17 warnings
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
Process completed with exit code 128.
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
Process completed with exit code 128.
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
Process completed with exit code 128.
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WDL test RUN_CNN_WDL on cromwell
Process completed with exit code 128.
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WDL test RUN_M2_WDL on cromwell
Process completed with exit code 128.
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
Process completed with exit code 128.
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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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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 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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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 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
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
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
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
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_CNN_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
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
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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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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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, google-github-actions/setup-gcloud@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/
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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, google-github-actions/auth@v0, google-github-actions/setup-gcloud@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/
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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, google-github-actions/auth@v0, google-github-actions/setup-gcloud@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/
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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 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, google-github-actions/auth@v0, google-github-actions/setup-gcloud@v0, 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, google-github-actions/auth@v0, google-github-actions/setup-gcloud@v0, 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, google-github-actions/auth@v0, google-github-actions/setup-gcloud@v0, 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, google-github-actions/auth@v0, google-github-actions/setup-gcloud@v0, 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-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
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2.25 GB |
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test-results-17.0.6+10-cloud
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333 KB |
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test-results-17.0.6+10-integration
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3.46 MB |
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test-results-17.0.6+10-unit
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157 MB |
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test-results-docker-17.0.6+10-conda
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282 KB |
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test-results-docker-17.0.6+10-integration
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3.38 MB |
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test-results-docker-17.0.6+10-unit
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155 MB |
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test-results-docker-17.0.6+10-variantcalling
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235 KB |
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