Missing chr20.germline.vcf from germline calling step

[briansha]

I'm using the example data from the documentation.

In v1.6.0 - the file chr20.germline.vcf does not get generated from the germline calling step.

${path}/src/Monopogen.py  germline  -a ${path}/apps  -r region.lst \
 -p ./  -t 22 \
 -g  GRCh38.chr20.fa  -m 3 -s all  -o bm

This file does, however, get generated in v1.0 of monopogen.

Since I'm running the Somatic SNV calling from scRNA-seq piece of Monopogen, the absence of this file seems to generate further issues downstream.

This needs fixed. In the meantime, I'll just have to try v1.5.0 and see if this issue persists.