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feat: Added option to pass custom WES Adapter environment variables

Open kankou-aliaksei opened this issue 2 years ago • 1 comments

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

kankou-aliaksei avatar Apr 29 '22 09:04 kankou-aliaksei

Looking forward to this so I can set config options as per https://github.com/chanzuckerberg/miniwdl/issues/570

nh13 avatar Jul 14 '22 18:07 nh13