Consider passing the annotation tool output to modules input for more standardization

[Darcy220606]

Description of feature

Currently, some modules take in .fna as an input rather than taking in .faa as an input from the annotation tool assigned. This might create diffrerences in the way prediction modules particular covering teh BGC and ARG workflows, because each module runs a different annotation tool. To standardise this more, i would suggest to consider checking the 'BGC and ARG' modules to ensure, if possible, that they take already annotated '.faa' files from the annotation tool.

• MACREL
• GECCO
• DEEPBGC
• all ARG tools