@Jose Espinosa-Carrasco I just had a thought to get around the resuming issue we talked about with the bracken module.... So you think a reasonable workaround would be too hard code the result directory as emitted by the module but to specify in meta.yaml yo customise

publishDir to use the prefix

variable to rename the directory? That way the user gets the standalone database directory with the right name, but keep resume (no

mv

command), and I don't think it will cause file collision in downstream modules because you can never use multiple databases in a single classification step

Yeah, I think is a good idea if the directories can't clash but when you say

meta.yaml

you mean

modules.config

, don't you?

No, as in I would have to document in

meta.yaml

that if you want to save the directory name as something different you will need to specify this via

publishDir

customisation NOT

prefix