Add option for GFF files

[ewels]

It could be nice to have an optional step to convert GFF to GTF files, to increase the range of inputs the pipeline can handle.

This can be done with the UCSC gffread tool:

./gffread my.gff3 -T -o my.gtf

xref SciLifeLab#229 (comment)

[apeltzer]

Conda package for gffread exists, so this can be done fairly straightforward: gffread

[apeltzer]

@aanil : Here you go: https://anaconda.org/bioconda/gffread

[ewels]

Closed in #52