Add missing essential parameters for antismash

[Darcy220606]

Description of feature

The new version of antismash requires essential parametrs that i would suggest to be included in the pipeline. Those are pfam2go --rre --tfbs at the moment i add them using ext.args in the default runs.

[jfy133]

@Darcy220606 does this still apply?

[jasmezz]

I added those params to the pipeline in the above PR.
@Darcy220606 Do you have more description than what is given by the antismash --help? The documentation gives nothing 🙃 It would be nice to fill the params help text a bit more, but it is not a must.

[Darcy220606]

I added those params to the pipeline in the above PR. @Darcy220606 Do you have more description than what is given by the antismash --help? The documentation gives nothing 🙃 It would be nice to fill the params help text a bit more, but it is not a must.

They all basically add more annotation to the BGC to allow for better selection for downstream experimental processing:

• pfam2go: maps the proteins to PFAM db.This helps annoate BGC modules with functional information based on the protein families they contain.
• rre: predicts regulatory elements on the BGC that help in teh control of expression of the peptides/proteins
• tfbs: predicts the transcription factor binding sites, again which helps in regulation of expression

[jasmezz]

Done in #403