Step 3: The Wuhan primer files are currently hardcoded here. Is this okay or should we do something different? about covid-19-signal

[fmaguire]

@kmsmith137 added this and most of the hardcoded paths to to the config.yaml and accesses them through that in Snakemake pipeline

So that and #6 #7 #9 can all be modified there as needed

[nknox]

can we have it accept a file similar to here: https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V3

[fmaguire]

This is related to #25 as the scheme requires changing how trimming is done.

If someone can generate a BED scheme for the wuhan primers we can just move entirely to this format.