Just noticed that we're wasting two hours indexing the fasta for BWA even when BWA isn't used because the index is listed as an input for the "mergeBWA" rule even if Pore-C data is input. "alignBWA" rules have if config['withPOREC'] == "False" else rules.emptyfile.output[0] for that input line, recommend adding that to the "mergeBWA rule as well