New RFC: use process directives to declare prefix, args and when defaults

[nvnieuwk]

Have you read the RFC docs?

• Yes, I have read and understood the RFC docs

Summary

Currently modules declare their prefix and args as defaults inside of the script: and stub: block which creates code duplication. Having the defaults as directives will deduplicate this code and make sure that stub and script blocks have the same defaults.

Champion

@nvnieuwk

Background & Motivation

I made a POC PR some time ago and am trying to get this through via an RFC.

Goals

• Reduce code duplication in processes
• Use more Nextflow native ways of handling ext directive defaults
• Update nf-core/tools linting to fail on when the old syntax is being used so the migration will happen progressively

Non-Goals

• Break modules, this change shouldn't have any effect on the current way we use modules

References

• POC: declare ext variable defaults as directives modules#8808
• https://nfcore.slack.com/archives/C043UU89KKQ/p1753349359402809

[nf-core-bot]

Approval status: 🕐 Pending

RFC has approvals from 5/7 required @nf-core/core quorum.

Review Status	Core Team members
✅ Approved	@maxulysse, @sateeshperi, @JoseEspinosa, @mirpedrol, @mribeirodantas
🕐 Pending	@ewels, @mashehu, @FriederikeHanssen, @kenibrewer, @jfy133, @edmundmiller, @FranBonath, @christopher-hakkaart, @nvnieuwk

[nf-core-bot]

Approval status: 🕐 Pending

RFC has approvals from 0/7 required @nf-core/core quorum.

Review Status	Core Team members
🕐 Pending	@ewels, @maxulysse, @mribeirodantas, @mashehu, @JoseEspinosa, @mirpedrol, @FriederikeHanssen, @kenibrewer, @jfy133, @edmundmiller, @sateeshperi, @FranBonath, @christopher-hakkaart, @nvnieuwk

[mahesh-panchal]

I like this. I hadn't thought of this in the initial implementation. 🚀

[maxulysse]

Is this an extension of #69 ?

[maxulysse]

Ooooh, I see, I like this

[maxulysse]

/approve

[nvnieuwk]

Is this an extension of #69 ?

Yeah kind of, but not entirely. This one will also need a default of course ;)

[mahesh-panchal]

Is this an extension of #69 ?

I see them as different things. I don't think suffix should be user configurable.

[sateeshperi]

/approve

[JoseEspinosa]

/approve

[mirpedrol]

/approve

I also like the idea :)

But I think we should add a couple of points to this RFC:

• Add linting to make sure that all modules follow this structure
• Update all modules (or fail linting and update them progressive - to discuss)

[mribeirodantas]

/approve