amrfinderplus improvements

[kapsakcj]

Based on this info: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus#input-file-formats

I think the amrfinderplus task can be improved greatly if we provide it a GFF as well as a protein FASTA along side the nucleotide FASTA (assembly).

We could alter the workflows to:

• run Bakta prior to amrfinderplus (make this default annotation tool, if not already)
• use Bakta GFF & AA FASTA outputs as input into amrfinderplus

[kapsakcj]

There's a bit more explanation here: https://github.com/ncbi/amr/wiki#methods

(and probably in the publications too, which I need to read)

but this could help identify novel sequences

for example...novel shiga toxin genes produced by STECs

[kapsakcj]

Now that v3.11.2 is available in a staphb docker image, we also need to make changes to the amrfinderplus task to accept new organism designations:

"Klebsiella_pneumoniae" and "Klebsiella_oxytoca"

"Neisseria_gonorrhoeae" and "Neisseria_meningitidis"

More details: StaPH-B/docker-builds#550 (comment)