Quality Checks before running

salvadorlab / mbovpan

Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.

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Quality Checks before running #19

Closed noahaus closed 10 months ago

noahaus commented 1 year ago

would be good to do some physical checks on the input to see if it is usable, at least to ensure that the sequences are actually m. bovis. Make this part of a parameter called careful

[x] add 'spotyping' functionality
[x] a quick diagnostic check if the input is paired (probably good enough to just ignore the ones that fail?
[x] update the main script

noahaus commented 10 months ago

Lineage Table created and now works with the the main code!