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VS-1422 Merge VAT changes in echo into ah_var_store #4679

VS-1422 Merge VAT changes in echo into ah_var_store

VS-1422 Merge VAT changes in echo into ah_var_store #4679

Triggered via pull request September 30, 2024 17:08
Status Success
Total duration 1h 16m 31s
Artifacts 8

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
40m 12s
build and push gatk docker to artifacts
Validate script WDLs using womtools
1m 9s
Validate script WDLs using womtools
Validate generated WDLs using womtools
13m 36s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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15 errors and 17 warnings
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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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
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The v0 series of google-github-actions/auth is no longer maintained.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
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The v0 series of google-github-actions/auth is no longer maintained.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
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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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
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The v0 series of google-github-actions/auth is no longer maintained.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
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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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
WDL test RUN_CNN_WDL on cromwell
Process completed with exit code 1.
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
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
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
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
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
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
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
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
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/
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/
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/
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/
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/
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/
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/
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/
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/
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_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_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/
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/
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/
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/
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/
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/

Artifacts

Produced during runtime
Name Size
gatkDockerImage
2.32 GB
test-results-17.0.6+10-cloud
333 KB
test-results-17.0.6+10-integration
3.46 MB
test-results-17.0.6+10-unit
157 MB
test-results-docker-17.0.6+10-conda
282 KB
test-results-docker-17.0.6+10-integration
3.39 MB
test-results-docker-17.0.6+10-unit
155 MB
test-results-docker-17.0.6+10-variantcalling
235 KB