Prioritize het calls when merging clustered SVs #4936
mwalker174gatk-tests.yml
on: pull_request
check if the environment has privileges
0s
build and push gatk docker to artifacts
16m 38s
Validate script WDLs using womtools
3m 30s
Validate generated WDLs using womtools
14m 48s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
7 errors and 14 warnings
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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The v0 series of google-github-actions/auth is no longer maintained.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 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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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 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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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 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The v0 series of google-github-actions/auth is no longer maintained.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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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_M2_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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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
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Java 17.0.6+10 build and test unit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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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
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
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 test on docker unit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Java 17.0.6+10 test on docker conda
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Java 17.0.6+10 test on docker variantcalling
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Java 17.0.6+10 test on docker integration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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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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2.22 GB |
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test-results-17.0.6+10-cloud
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268 KB |
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test-results-17.0.6+10-integration
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3.53 MB |
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test-results-17.0.6+10-unit
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86.3 MB |
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test-results-docker-17.0.6+10-conda
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294 KB |
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test-results-docker-17.0.6+10-integration
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3.46 MB |
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test-results-docker-17.0.6+10-unit
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84.9 MB |
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test-results-docker-17.0.6+10-variantcalling
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243 KB |
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