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asapdiscovery / choppa

Integrated mutational and structural biology data into a concerted HTML view.
MIT License
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Add Nextstrain functionality #42

Closed JenkeScheen closed 1 month ago

JenkeScheen commented 3 months ago

With CLI endpoint so that we can download gene mutation data from https://nextstrain.org/pathogens#list

JenkeScheen commented 1 month ago

@hmacdope this is now working for all viruses/genes that we have available in https://github.com/asapdiscovery/choppa/blob/nextstrain/choppa/data/metadata/nextstrain.json. There are a few viruses that we'd like to include (MERS-CoV, WNV) but their NextStrain entries are too borked (gene nomenclature is way off).

Can you check why CI is failing here and review plz?