Generally, I found it would also be great to be able to skip some of the pre-processing steps (eg. BAM_QC, CELLSNP_MODEA) upon user choice and the memory requirements could probably be reduced

You are absolutely right. I am currently testing the pipeline with a large data set and am encountering the same issues. However, you can already skip

BAM_QC

and

CELLSNP_MODEA

. Just set `--bam_qc` to false. We need

CELLSNP_MODEA

for find_variants and vireo. So you have to set `--find_variants` to false and remove vireo from

--genetic_tools

if you want to skip

CELLSNP_MODEA

.