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theiagen / public_health_bacterial_genomics

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float Kleborate/K pnemoniae K & O locus calls to Terra table #142

Closed kapsakcj closed 2 years ago

kapsakcj commented 2 years ago

Currently, the kleborate task calls the kaptive tool to determine the K and O locus types but the outputs are only available in the kleborate_output_file TSV.

It would be nice if these calls were parsed from the TSV and floated to the Terra data table.

Columns to include (example):

might be other columns to include, but I think these would be the most useful

CC @frankambrosio3

kapsakcj commented 2 years ago

Also would be good to update to kleborate v2.2.0. Currently, 2.0.4 is the default version

I'm working on making a staphb docker image for 2.2.0. Should be ready shortly

kapsakcj commented 2 years ago

New docker image for v2.2.0 available on dockerhub and quay:

https://hub.docker.com/r/staphb/kleborate/tags

staphb/kleborate:2.2.0

kapsakcj commented 2 years ago

started a dev branch for this - cjk-kleb-output-parsing

ran successfully via miniwdl, testing in Terra now

kapsakcj commented 2 years ago

closed via #148