nextstrain / measles

Nextstrain build for measles virus
https://nextstrain.org/measles
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Assign genotypes using Nextclade dataset and visualize on tree #36

Closed kimandrews closed 4 weeks ago

kimandrews commented 1 month ago

Description of proposed changes

This PR does the following:

  1. Uses the Nextclade dataset during ingest to assign MeV genotypes to each sequence. Genotype assignments and other Nextclade output are added as columns to the metadata output.
  2. Adds MeV genotype coloring to the N450 and genome trees (https://nextstrain.org/measles/N450 and https://nextstrain.org/measles/genome).
  3. Updates the metadata for the phylogenetic workflow example data to match the new ingest metadata output format.

The Nextclade dataset is currently on the "master" version of Nextclade dataset server. After it is released, we can remove --server=https://data.master.clades.nextstrain.org/v3 from the get_nextclade_dataset rule.

This PR addresses https://github.com/nextstrain/measles/issues/32

Related issue(s)

https://github.com/nextstrain/measles/issues/32

Checklist

trvrb commented 1 month ago

Looks great to me. In testing, this just worked locally as well.