switch primer/genome syntax to the more generic `--fasta` and `--bed`?

[tavareshugo]

Currently we use this kind of syntax to specify the genome and primer scheme:

--genome 'MN908947.3' \
--primer_set artic \
--primer_set_version 3

This is equivalent to (links from artic repo):

--fasta https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta \
--bed https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed

Advantages of the latter syntax:

• Can also be used using local files (i.e. the files can be downloaded beforehand).
• Allows using other reference genomes (e.g. other viruses) or custom primer schemes.
• Doesn't depend on viralrecon developers to have made the primer scheme you are using available. For example, do you want to use NEB VARSkip primer set "2b"? You can get them from their repo and then specify:

--fasta https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V2b/NEB_VarSkip.reference.fasta \
--bed https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V2b/NEB_VarSkip.scheme.bed