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ellisrichardj / BovTB-nf

Nextflow script for processing WGS data
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Genotype inference #2

Closed ellisrichardj closed 5 years ago

ellisrichardj commented 5 years ago

This part of the process needs work, both on the nextflow pipeline and the underlying python script to run correctly

ellisrichardj commented 5 years ago

One of the issues seems to be that calling gunzip from within the python script results in an empty vcf being created. However, 'gunzipping' the vcf.gz before running the python script works OK

ellisrichardj commented 5 years ago

Superseded by #5