begin sketching up pipeline for #30 [ci skip]
snakemake fixes [ci skip]
more updates [ci skip]
more filling out of depletion pipe [ci skip]
fix a rule [ci skip]
fix a rule [ci skip]
more attempts to fill out the pipe [ci skip]
fix? [ci skip]
more snakemake fixes [ci skip]
clean json [ci skip]
pull out some more hardcoded stuff into config.json [ci skip]
cleanups [ci skip]
update command signature [ci skip]
small tweaks [ci skip]
update pipes to new command interfaces, make read_utils executable [ci skip]
remove unnecessary paths to executables [ci skip]
not related to hs depletion, but start tweaks for assembly pipeline [ci skip]
fix pattern matching and generalize [ci skip]
correct wildcard notation [ci skip]
convert dynamic to fixed expansion [ci skip]