VS-1007 - Use default names for VQSR-Lite generated code. #2778
gbggrantgatk-tests.yml
on: pull_request
check if the environment has privileges
1s
build and push gatk docker to artifacts
23m 3s
Validate script WDLs using womtools
4m 10s
Validate generated WDLs using womtools
14m 16s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
2 errors and 58 warnings
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Java 11 build and test cloud
Process completed with exit code 1.
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Java 11 build and test integration
Process completed with exit code 1.
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check if the environment has privileges
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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Validate script WDLs using womtools
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Validate script WDLs using womtools
Unexpected input(s) 'fetch', valid inputs are ['repository', 'ref', 'token', 'ssh-key', 'ssh-known-hosts', 'ssh-strict', 'persist-credentials', 'path', 'clean', 'fetch-depth', 'lfs', 'submodules', 'set-safe-directory']
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Validate script WDLs using womtools
Unexpected input(s) 'fetch', valid inputs are ['repository', 'ref', 'token', 'ssh-key', 'ssh-known-hosts', 'ssh-strict', 'persist-credentials', 'path', 'clean', 'fetch-depth', 'lfs', 'submodules', 'set-safe-directory']
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Validate generated WDLs using womtools
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Validate generated WDLs using womtools
Unexpected input(s) 'fetch', valid inputs are ['repository', 'ref', 'token', 'ssh-key', 'ssh-known-hosts', 'ssh-strict', 'persist-credentials', 'path', 'clean', 'fetch-depth', 'lfs', 'submodules', 'set-safe-directory']
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Validate generated WDLs using womtools
Unexpected input(s) 'fetch', valid inputs are ['repository', 'ref', 'token', 'ssh-key', 'ssh-known-hosts', 'ssh-strict', 'persist-credentials', 'path', 'clean', 'fetch-depth', 'lfs', 'submodules', 'set-safe-directory']
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build and push gatk docker to artifacts
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38, docker/setup-buildx-action@v1, docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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WDL test RUN_CNN_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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WDL test RUN_M2_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Java 11 build and test unit
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
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Java 11 build and test unit
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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Java 11 build and test unit
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test unit
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Java 8 build and test cloud
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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Java 8 build and test cloud
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 build and test cloud
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 build and test cloud
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Java 11 build and test cloud
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Java 11 build and test integration
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Java 8 test on docker conda
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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Java 8 test on docker conda
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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Java 8 test on docker conda
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
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Java 8 test on docker conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/download-artifact@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Java 8 test on docker variantcalling
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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Java 8 test on docker variantcalling
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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|
Java 8 test on docker variantcalling
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 test on docker variantcalling
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/download-artifact@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
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Java 8 test on docker unit
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 test on docker unit
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 test on docker unit
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 test on docker unit
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/download-artifact@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Java 8 test on docker integration
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 test on docker integration
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 test on docker integration
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 test on docker integration
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/download-artifact@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
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gatkDockerImage
Expired
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2.27 GB |
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test-results-11-cloud
Expired
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251 KB |
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test-results-11-integration
Expired
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4.49 MB |
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test-results-11-unit
Expired
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63.1 MB |
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test-results-8-cloud
Expired
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250 KB |
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test-results-docker-8-conda
Expired
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286 KB |
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test-results-docker-8-integration
Expired
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4.48 MB |
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test-results-docker-8-unit
Expired
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67.3 MB |
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test-results-docker-8-variantcalling
Expired
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184 KB |
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