Add support for using GFF instead of GTF

[milos7250]

I thought it would be a nice addition to have the option to use GFF files as well as GTF files when specifying references. I was inspired by the rnaseq pipeline and added the conversion from GFF to GTF.

I have tried this on a small dataset using barley genome and it worked well. For a complete PR I think this would require adding one test where a GFF is supplied instead of a GTF.

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