(Possibly) refactor index construction

[tskir]

Ii've not addressed this particular comment because having bot process in one causes some issue in the output channel. (specifically the order in the output channel needs to be known so that the right .fai can be used)

This might be due to my limited understanding of how nextflow works at this time but for now I would rather keep the explicit duplication.

About the second point. There is always a risk about using externally constructed index (with samtools/bowtie or others) but most tools have been pretty good at not changing their indexes between version. So the risk is limited and the saving in time and resources can be big.

Originally posted by @tcezard in #9

There are two points here:

• Getting rid of possible code duplications
• Looking into whether reusing external indexes is always safe