Accept GZipped FASTA files as reference

[jfy133]

Is your feature request related to a problem? Please describe.
Eukaryotic genomes can sometimes be large and can take a up lot of space when in uncompressed formats.

We could consider accepting .fasta.gz files, as with the FASTA files.

For indexing this would require a decompressing, indexing then re-compression step of the FASTA itself - but indices are often smaller so I guess wouldn't require indexing.

The only potential issue I see here is how the pipeline deals with multiple runs trying to access the same file at once.