update the gff2json.py to integrate into nextflow

[anwarMZ]

Is your feature request related to a problem? Please describe. The gff2json.py script requires a dictionary file. This is a cumbersome step. For example for mpox

{
  "reference": "Nigera-2018",
  "accession": "NC_063383.1",
  "species": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10244",
  "genome": "ACTG"
 }

Describe the solution you'd like This can be removed by providing the

• [x] reference: can be a string provided or use the accession
• [x] accession: can be parsed from the reference genome fasta file (which is always going to be available)
• [x] species: already available in the gff file. starting with ##
• [x] genome: can be parsed from the reference genome file

example updated usage - usage: gff2json.py [-h] [--gff_file GFF_FILE] [--ref_fasta FASTA] [--output_json JSON] [optional; --colors_scheme JSON]

[anwarMZ]

Removing the genome key from the output fasta file so we don't need the fasta file as an argument.

• [x] accession can be parsed from the input gff file.

[anwarMZ]

For the colors, intergenic is grey by default