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nf-core / tools

Python package with helper tools for the nf-core community.
https://nf-co.re
MIT License
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nf-core modules create tool/subtool should make a main.nf in a subfolder of subtool in pipelines #3251

Closed mahesh-panchal closed 5 days ago

mahesh-panchal commented 5 days ago

Description of feature

When writing local pipeline modules, using nf-core modules create tool/subtool, it follows a different file structure to the standard modules file structure. It would be nice if local pipeline modules followed the same file format as nf-core modules.

Rather than

modules/
    local/
        tool/
            subtool.nf

It should be

modules/
    local/
        tool/
            subtool/
                main.nf

The environment.yml is also missing as a result of this.

Alternative

Turn everything on it's head in nf-core modules and each module should be in a subtool.nf file, meaning only a single (all encompassing) environment.yml is needed for all subtools ( which also rearranges tests, etc )

mirpedrol commented 5 days ago

Hi @mahesh-panchal, thanks for the issue! This is a duplicate of https://github.com/nf-core/tools/issues/1929 and it's already in the roadmap 🙂

mahesh-panchal commented 5 days ago

Thanks. I guess I didn't use the right words when searching.