I am going to use the #CE9MS66BS and after I want to pass the results into #C02K5GX2W93, should I add `--skip_prokka`and `--skip_prodigal`in the #CE9MS66BS so I dont repeat the work? Is there a specific way to signal de pipelines that you will be using other pipelines next so the files are already in the correct format?

The former, yes - but if you want to use prokka/prodigal (and not e.g. bakta), you could even let mag do the annotation, and you can pass the annotation files already to funcscan 🙂 'Either way around' works basically

Great thanks!