nextstrain / measles

Nextstrain build for measles virus

https://nextstrain.org/measles

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Connect ingest and phylogenetic workflows to follow pathogen-repo-guide #19

Closed kimandrews closed 3 months ago

kimandrews commented 3 months ago

Description of proposed changes

Connect ingest and phylogenetic workflows, following the pathogen-repo-guide:

Upload ingest output to S3
Download ingest output from S3 to phylogenetic directory
Use accession column as ID column for phylogenetic analysis (addresses this github issue: #11)
Add color scheme matching the new region name format

This PR focuses on making changes that are necessary to move forward with creating a locus-specific workflow in a later PR.

Related issue(s)

11

Checklist

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