Allow viralrecon to take gtf as input annotation file

[svarona]

Description of feature

We are working on a custom gtf file with multiple overlapping features for SARS-CoV-2, but viralrecon won't let you use a gtf file as annotation file.

Depending if the input annotation file is a gff or a gtf, SNPEFF_BUILD process should be changed, because now it only works for gff files:

viralrecon/modules/local/snpeff_build.nf

Line 49 in 23e3441

-gff3 \\

Also, some additional changes are needed in the make_variants_long_table.py to allow overlapping features to appear in the results table.

An example of the original variants_long_table output:

An example of the table we want to obtain: