ingest: Remove use of ncov-ingest geolocation rules #79
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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:
There were less changes than I had expected and I realized it's because there are many annotations already updating the 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. |
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Will merge this tomorrow if there are no comments. |
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This is a really nice improvement to our analysis.
P.S. There are no New Caledonia sequences in the staging dataset. Since there are n=8 originally it's possible they were all excluded by the subsampling (especially if the 8 samples were well spread temporally), and I presume this is what happened, but perhaps double check?
Thanks for flagging! Looks like all of the New Caledonia sequences are filtered out because they have length less than the min_length. |
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