Consolidate bwa and .fai indexes in reference workflow

[lkhilton]

I have a tool that depends on having both bwa and .fai indexes for the reference genome in the same directory, so the first rule I had to write was one that symlinked the files together. In future versions of the reference file workflow I think it would be good to place the different index types together in one directory per genome build.

[Kdreval]

@lkhilton this is probably addressed by now? Or is something still missing?