amazon-genomics-cli
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feat: Added option to pass custom WES Adapter environment variables
Issue #: https://github.com/aws/amazon-genomics-cli/issues/396
Description of Changes
[//]: # This adds option to pass custom environment variables into WES Adapter [//]: # This adds option to pass custom environment variables into Workflow Job
Description of how you validated changes
[//]: # Add configuration for context
contexts:
miniContext:
customWesEnvVars:
- key: k1
value: v1
- key: CUSTOM_WORKFLOW_JOB_ENV_VARS
value: "[{ \"key\": \"MINIWDL__AWS__BOTO3_RETRIES\", \"value\": { \"max_attempts\": 15, \"mode\": \"standard\" } }, { \"key\": \"MINIWDL__AWS__DESCRIBE_PERIOD\", \"value\": 10 }, { \"key\": \"MINIWDL__AWS__SUBMIT_PERIOD\", \"value\": 10 }]"
engines:
- type: wdl
engine: miniwdl
[//]: # Deploy context agc context deploy --context miniContext [//]: # After context deploying a WES Adapter Lambda must have k1 and CUSTOM_WORKFLOW_JOB_ENV_VARS env vars [//]: # After agc workflow run hello --context miniContext go to Batch Workflow Job Logs and find MINIWDL__AWS__BOTO3_RETRIES, MINIWDL__AWS__DESCRIBE_PERIOD, MINIWDL__AWS__SUBMIT_PERIOD vars under === ENVIRONMENT === section
Checklist
- [x] If this change would make any existing documentation invalid, I have included those updates within this PR
- [x] I have added unit tests that prove my fix is effective or that my feature works
- [x] I have linted my code before raising the PR
- [x] Title of this Pull Request follows Conventional Commits standard: https://www.conventionalcommits.org/en/v1.0.0/
By submitting this pull request, I confirm that my contribution is made under the terms of the Apache-2.0 license
Looking forward to this so I can set config options as per https://github.com/chanzuckerberg/miniwdl/issues/570