Hi! Im currently facing an issue with nf-core modules lint running in CI: https://github.com/nf-core/modules/actions/runs/12058261501/job/33624622077?pr=7107 Im trying to push a new nf-core module called "compute_gene_scores" which contains an R script in the resources/usr/bin as detailled in https://www.nextflow.io/docs/latest/module.html#module-binaries But the CI tests are trying to run the following: nf-core modules lint compute_gene_scores/resources nf-core modules lint compute_gene_scores/nextflow.config Both of which are failing, because those are not actual modules, but files in the new module. Has anyone seen this before and could indicate what I'm doing wrong? Note: The PR includes two nf-core modules and a new subworkflow, when linting the subworkflow I get an issue where it converts underscores to forward slashes and complains that the modules are not included (the modules names are "compute_gene_scores" and "create_gene_heatmap"):

Cc @Sateesh_Peri if you are still around

You can't have underscores in module names

You can't have underscores in module names

@Arthur not sure if that is true. every tool suite with subtools will have underscores https://github.com/nf-core/methylseq/blob/d16f8f81e812d86f4d297e69de3f001628dfd5b4/modules/nf-core/bismark/methylationextractor/main.nf#L1 or did i misread you ?

the underscore between tool/subtool is rendered by the template only where the

/

would be. When I look at the PR it seems that the module folder has an underscore in it? That is not allowed

@Nicolás Alejandro Schcolnicov are you trying to modularize this nanostring pipeline ?

@Sateesh_Peri Yes, im trying to modularize nanostring. I'll check what you mentioned about removing underscores, thank you! @Arthur Do you think it is probably not worth adding into nf-core? I know it isn't actually a tool, but it could still be helpful for others wanting to do this same analysis.

I would personally suggest that for now this is better kept as a local module in

nanostring

. I would convert them to local modules which have the

nf-core/modules

format though (i.e. no underscores in name, and in their own folders with

<http://main.nf|main.nf>

,

meta.yml

etc) That way you can move them to

nf-core/modules

more easily in future if there is a desire to use them outside of

nanostring

Exactly my thought, that way I also don't waste the time I already invested in formatting them into nf-core standards. Thanks everyone!

FWIW there is a PR to address the open issue of unifying local module structure with the remote structure

> Has anyone seen this before and could indicate what I’m doing wrong? You are not doing anything wrong. The CI is broken at the moment. I have already spent a couple of hours racking my brain over this (see the post just above yours). Edmund is thankfully working on a fix already.