Tools (mosdepth, indexcov, covviz, somalier) should run only for samples supplied in input pedigree file
The following discussion from !1 (merged) should be addressed:
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@bwilk777 started a discussion:
Think through things this will have to be changed to only run on samples specified. Due to the directory structure/accessioning system we set up RNASeq and DNASeq data all end up in the same place and I imagine this would mess things up here for sure. Would also be good because I'm guessing some sort of QC specific for RNASeq data will get added into this setup at some point in the future as well.