Different genomes for BWA-MEM2 and HISAT2

[tyamaguchi-ucla]

But for outside users, we can't expect that they have indices for both BWA-MEM2 and HISAT2 in the same folder, right?

This is up to us since it looks like the index files don't overlap. I don't think we want to allow users to use different reference genomes if possible. Let me create an issue and discuss there as this is not related to this PR.

Originally posted by @tyamaguchi-ucla in #146 (comment)