Update Beta User WDL to use bulk ingest [VS-982] #2707
rsasch
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gatk-tests.yml
on: pull_request
check if the environment has privileges
0s
build and push gatk docker to artifacts
20m 20s
Validate script WDLs using womtools
3m 28s
Validate generated WDLs using womtools
14m 56s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
5 errors and 47 warnings
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Java 8 test on docker conda
Process completed with exit code 1.
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WDL test RUN_CNN_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
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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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/
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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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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/
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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/
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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 `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 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 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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Java 11 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 11 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 11 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/
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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/
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Java 11 build and test 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/
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Java 11 build and test 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/
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Java 11 build and test 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/
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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/
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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/
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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/
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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/
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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/
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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/
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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/
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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/
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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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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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247 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 MB |
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test-results-8-cloud
Expired
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246 KB |
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test-results-docker-8-conda
Expired
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1.14 MB |
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test-results-docker-8-integration
Expired
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4.5 MB |
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test-results-docker-8-unit
Expired
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67.4 MB |
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test-results-docker-8-variantcalling
Expired
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182 KB |
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