GitHub Action workflows clean up #218
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Recently learned that Snakemake no longer overwrites the entire config when providing nested config values via the `--config` option.¹ This allows us to remove the set-branch-ingest-config script and directly set branch config values via the command line option in our GitHub Action workflows. I've opted to use `jq` to interpolate the branch name into the S3_DST because I didn't want to fiddle with escaping quotes in the JSON string. ¹ nextstrain/dengue#13 (comment)
Since we've removed the need to run set-branch-ingest-config in the GitHub Action workflow in the previous commit, we can refactor the fetch-and-ingest-branch workflow to use the shared pathogen-repo-build workflow.
The AWS_DEFAULT_REGION envvar is not required for AWS S3 interactions, so remove it from our workflows and documentation. This will allow us to remove AWS_DEFAULT_REGION from the repo secrets so that our pathogen-repo-build summary no longer points to a masked URL for the AWS Batch console (e.g. https://console.aws.amazon.com/batch/home?region=***#jobs/detail/0d66a150-a010-4761-9561-8085ef1d7ea3).
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As part of this PR, I've already removed the |
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The GITHUB_RUN_ID environment variable is only used for Slack notification messages, so it is not needed for the branch workflows that run without Slack notifications.
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Clean up GitHub Action workflows, see commits for details.
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