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andersen-lab / Freyja

Depth-weighted De-Mixing
BSD 2-Clause "Simplified" License
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Allow user to pass in lineages.yml #165

Closed wutron closed 8 months ago

wutron commented 1 year ago

Can lineages.yml be passed through an argument, perhaps --hierarchy? This functionality would match allowing the user to pass through --barcodes and --meta. From a cursory look, demix, boot, plot, and relgrowthrate use this file.

ktmeaton commented 8 months ago

Just giving this issue a bump. This gets me everytime I upgrade to a new --barcodes and --meta, but forget to run freyja update to make sure the internal lineages.yml is synchronized 😅

joshuailevy commented 8 months ago

Thanks for the reminder! Was just looking back into this (sorry for the delay!!)- we'll have it added in soon!