nextstrain / seasonal-flu

Scripts. config, and snakefiles for seasonal-flu nextstrain builds
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Update builds to use `--env` options #118

Closed joverlee521 closed 1 year ago

joverlee521 commented 1 year ago

Description of proposed changes

Better to be explicit about which envvars are being passed to runtimes rather than rely on the automatic variables passed through.

The upload workflow requires the rethinkdb secrets to access Fauna and the AWS secrets to upload files to S3.

The public and private builds just need the AWS secrets to launch jobs on AWS Batch and to download files from S3.

These are all GitHub Action secrets that are being inherited by the reusable workflow and available as envvars in the GitHub Action job.

Related issue(s)

Follow up on https://github.com/nextstrain/seasonal-flu/pull/111, following @tsibley's recommendation to be explicit about envvars.

Testing