Having UMItags : FALSE in the configuration gets the umitags rule excluded when the Snakefile is parsed, but there's still a later rule (core_stat_matrix in arch.rules) that expects {sample}.umitags.stat as input. Would some sort of call to WriteNullOutput to make stub .stat files do the trick for UMItag-less runs, maybe? I'm trying right now just touching empty files but I expect that'll confuse core_stat_matrix when it gets there.
Having
UMItags : FALSE
in the configuration gets the umitags rule excluded when the Snakefile is parsed, but there's still a later rule (core_stat_matrix in arch.rules) that expects {sample}.umitags.stat as input. Would some sort of call to WriteNullOutput to make stub .stat files do the trick for UMItag-less runs, maybe? I'm trying right now just touching empty files but I expect that'll confuse core_stat_matrix when it gets there.