Hi! I have a questions concerning nf-core/modules in general (I guess it's been answered somewhere already but I don't really know how to search that...). What happens if a module is already registered in nf-core as <module> but someone wants to divide it into subsections, like <module>/<command> ? I am facing this issue with medaka: https://nf-co.re/modules/medaka/ Ideally, I would like to turn the existing medaka module into medaka/consensus and add other modules related to other subcommands. Thanks!

Ohhh, that's always a nice question

I don't think we have a specific procedure for this scenario, but what I would try is: • add the subcommands as subdirectories in the module directory, leaving the original files intact • open a deprecation procedure for the non-subcommanded module to give devs time to adapt to the change (nb: removing a module does not break pipelines, but does break update attempts)

We did that for several modules already

That totally makes sense

Thanks!

here what it can look like: https://github.com/nf-core/modules/blob/01bfb37b27aaba4bf595115f0e0e8cc196940ab7/modules/nf-core/deepvariant/main.nf#L4