Is CELLSNP maybe a new addition ? Its also not mentioned in the README overview image of the pipeline - would be great to know why its generally required if it is

See: https://nfcore.slack.com/archives/C067K2P6GUV/p1773392345572519?thread_ts=1773240146.577539&cid=C067K2P6GUV The overview image is from the legacy pipeline. We skipped updating the image due to time constraints. Based on my feedback to

CELLSNP

, how would you update the

README.md

? Is a small explanation text enough?

Ok I see - so for me it was unclear that if you input a VCF file, it would still by default search for variants (

--find_variants true

). I guess CellSNP prioritzies certain variants out of the input VCF? Maybe you could add a sentence on CellSNP in the "usage" section after explaining the input VCF. maybe sth like _"some tools such as vireo depend on refined sets of variants. Set --find_variants to false if the genotype does not need to be further refined."_ ?

--find_variants

should mean something else here. During donor matching, the pipeline can also determine two subsets of <http://(https://hadge.readthedocs.io/en/latest/rescue.html#~text=Whether%20to%20extract%20a%20subset%20of%20informative%20variants%20when%20best%20genotype%2Dbased%20method%20for%20donor%20matching%20is%20vireo.%20default:%20subset%20as%20described%20in%20paper;%20vireo:%20subset%20by%20Vireo;%20True:%20subset%20using%20both%20methods;%20False:%20not%20extracting%20variants.%20Default:%20False|informative variants> (`default`: subset as described in paper; `vireo`: subset by Vireo). Does that make it clearer? The relevant part in the paper The relevant part in the legacy docs

Ok I see yes that makes sense