freyja barcode-build

Build barcodes from a custom protobuf tree

freyja barcode-build [OPTIONS]

Options

--pb <pb>

protobuf tree

Default:

Sentinel.UNSET

--outdir <outdir>

Output directory save updated files

Default:

Sentinel.UNSET

--redo

Allow for overwriting of output directory

Default:

False

--noncl

only include lineages that areconfirmed by cov-lineages

Default:

True

--pathogen <pathogen>

Pathogen of interest

Default:

SARS-CoV-2

Options:

SARS-CoV-2 | MPXV | H5NX | H5NX-cattle | H1N1pdm | FLU-B-VIC | H3N2 | MEASLESN450 | MEASLES | RSVa | RSVb | DENV1 | DENV2 | DENV3 | DENV4 | manual

--format <format>

Default:

feather

Options:

feather | csv