I'm writing a subworkflow that I intend to contribute to the nf-core collection in due time. This of course means that the individual modules should also be submitted if they're not already there. However, there is at least one step that is highly specific for the subworkflow (checking that sequence names in the two types of input files are the same). Would it be OK to include a process definition in the swf?

does it need to be a module?, can you do that in groovy and have it in a function?

I think it needs to be a process/module. I was considering the groovy option, but I'm afraid certain cases might use a bit too much memory to inline in the Nextflow code. Moreover, there are three different file formats involved for the same type of file. (Since yesterday, other tasks that would be difficult to implement in groovy have also come up.)

how does it look like for now?

Not implemented yet. I was uncertain about what was the best way of doing this, so I postponed and started on other things.

I'd say that's why we have custom

Yeah, I have a couple of subworkflows with modules like that and make use of custom.

So, what do you mean with "custom"?

Just a directory of modules without much potential for reuse outside a particular swf?

Not just that, they're anything that doesn't belong to a specific software suite

Right, that makes more sense. thanks.