Fix Clade I build #284
Fix Clade I build #284
Conversation
Use `--query` to filter to Clade I and children clades since we have migrated to Nextclade v3 that includes clades I, Ia, and Ib. Resolves #283
Add an explicit `query` config param to make it clear that this is used for the `--query` option of `augur filter`.
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Trial build deployed to https://nextstrain.org/staging/trial/fix-clade-i/mpox/clade-I |
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I compared the trial build to the current live build and I'm confident in these changes so I'm going to merge. Summary of comparison: The trial build has one extra sequence (PQ221596/23MPX0047C), but all other sequences are the same based on accession. PQ221596 was previously unassigned with Nextclade v2, but is now assigned to clade Ia with Nextclade v3. So inclusion of PQ221596 in the trial build is expected. I noticed that the trial build clade assignments are slightly different than the live build in tangletree: 
I re-ran the build locally and the clade assignments are the same as the live build: 
I'm going to attribute this to some stochastic tree building weirdness that is not a result of any changes in this PR. |
Description of proposed changes
Use
--queryto filter for clade I build since we have migrated to Nextclade v3 that includes clades I, Ia, and Ib.Related issue(s)
Follow up to #281
Resolves #283
Checklist