Refactor case counts workflow #102
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The case counts scripts used csvtk before csvtk was officially added to nextstrain/docker-base so I worked around this by just running them directly in the GH Action workflow. Our push to use short-lived AWS credentials has finally pushed me to put this into a proper Snakemake workflow.
Refactored to use the shared `pathogen-repo-build` GH Action workflow so that it can use the short-lived AWS credentials that are automatically set up within the workflow.
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Description of proposed changes
Our push to use short-lived AWS credentials has finally pushed me to put this into a proper Snakemake workflow
that can be run by
nextstrain build.Related issue(s)
Related to https://github.com/nextstrain/private/issues/110
Checklist