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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
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[TheiaCoV] Isolate nextclade_v3 task for flu so that we can have outputs for HA and NA segments clearly identified #409

Closed cimendes closed 3 months ago

cimendes commented 5 months ago

:cool:

:pushpin: Explain the Request

Currently the nextclade outputs for flu only identify in the name of the segment for NA. For HA everything gets populated to the data table as just nexclade_tsv or nextclade_clade. It would be super helpful for the user to know that these refer to the HA segment.

This could be done by creating a third call of nextclade within theiacov, therefore having a nextclade call for all single-segment viruses (sc2, mpox, rsv-a, rsv-b) and have isolated for flu a nextclade_ha and nextclade_na.