snakemake define folder as output

Question

I try to run prokka using snakemake and rule all. In the latter I define all output folders which will be produced by prokka to write the results. Prokka requires a folder t

Answer 1

As @JohnnyBD mentioned, your major problem appears to be with rule all output not matching rule prokka. If you still need to use directory as output instead of a file, you may want to use directory() as it better handles edge cases.