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Curate standard geolocation rules #1488

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joverlee521 opened this issue Jun 25, 2024 · 1 comment
Open

Curate standard geolocation rules #1488

joverlee521 opened this issue Jun 25, 2024 · 1 comment

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@joverlee521
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Originally part of #1003, but this is a much bigger task than just porting over an existing script!

We have a great list of manually curated geolocation rules in ncov-ingest that our pathogen-repo-guide points to as the "general" geolocation rules, but these should really be curated down to a standard set of geolocation rules in augur.

@victorlin
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Various repos are referencing https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv directly. This makes it fragile to nextstrain/ncov-ingest#449 or any other renames. A couple things that could be done here without involving any curation work:

  1. Copy the file into the Augur repo
  2. Update references to use the file in Augur with - alias to the default branch

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