ingest: Remove use of ncov-ingest geolocation rules #303
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Remove the use of the ncov-ingest geolocation rules since Augur now uses the built-in geolocation rules by default. Depends on the release of <nextstrain/augur#1745>
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Tested locally with my local version of Augur that includes the changes from nextstrain/augur#1745 Diffed the output with the prod metadata, with expected changes to geolocation fields:
Ran the results through the phylogenetic workflow with the Augur changes The build has been uploaded to staging. Since subsampling includes grouping by country, there are more sequences now that samples from Puerto Rico are grouped separately than samples from USA. |
17 tasks
Following changes in geolocation rules in previous commit, Puerto Rico is now included at the country level.
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Description of proposed changes
Remove the use of the ncov-ingest geolocation rules since Augur now uses the built-in geolocation rules by default.
Depends on the release of
nextstrain/augur#1745
Related issue(s)
Part of nextstrain/public#17
Checklist