I opened this PR to introduce bwa-mem3 to the pipeline. Users can add

--compat=bwa-mem2

to

ext.args

for BWAMEM3_ALIGN to get alignment records identical to bwa-mem2 v2.2.1 (the PG header line still names bwa-mem3, so output files are not byte-identical). I'm also happy to include a more explicit switch if the team prefers that strategy.