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.
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.
Description of proposed changes
This PR does the following:
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 theget_nextclade_dataset
rule.This PR addresses https://github.com/nextstrain/measles/issues/32
Related issue(s)
https://github.com/nextstrain/measles/issues/32
Checklist
--server=https://data.master.clades.nextstrain.org/v3
from theget_nextclade_dataset
rule after measles Nextclade dataset is released