Question about -f and -v input file?

[YAYA530]

I'm confused a little bit about the input fils -f: input genomes/scaffolds and -v: prophage coordinates input from VIBRANT. I want to analyze the activation prophage in several case/control samples but I'm not sure if input scaffolds and prophage coordinates files are individual sample or these two files should combine all samples' scaffold together (like a database)?
So far, I finished reads assembly into scaffold in each sample. May I know whether I should combine all samples' scaffold together and do VIBRANT then do PropagAtE OR I should do VIBRANT and PropagAtE in each samples' assembly files?

[KrisKieft]

You can do either option mentioned. It depends on what you are interested in identifying/studying and what you hope to accomplish from your data. Based on the information given, I'd suggest running VIBRANT and PropagAtE separately on all samples (option 2).