A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Are we outputting yml files via the version topics channels now, or at least allowing them where the eval thing doesn't work? <https://github.com/nf-core/modules/pull/10873>

Yes there's an exception for modules using templates. Those should still use the yaml files but pass them to the topic

what would be the other way to deal with this?
modules binaries and we execute as bash?

OK good, does the boilerplate pipeline template code handle that?

iep, but if we had it, that would be the solution

&gt; what would be the other way to deal with this?
Running the scripts as a CLI tool

Yep, templates are just the least-worst way of doing module-level custom scripting right now. We should ditch them as soon as we have a better way.

Can we transfer custom scripts to some repo (`nf-core/modulescripts`?) and package them so they can be easily built into a container?

It's exactly what I did for the 'shinyngs' modules- baked scripts into an external, released repo. But the loop is long to make edits, you end up doing loads of releases of that external repo, I don't think we can force it as a standard.

maybe we can do that for scripts that we know are stable

I'm sure we have a couple of those in the modules repo

No, I don't like it as a thing, we'd end up with a million one-script repos

Some CI-based workaround where we pre-bake containers with scripts in is probably the way to go, and it's been talked about a bit

Could also add a tools feature to handle staging scripts from module binaries directly into `bin/`?

Here's the last time this was discussed: <https://nfcore.slack.com/archives/C04QR0T3G3H/p1769678574070939>

<@U03R5TJ77GF> - could you add your voice there? I'd love for Ben to hear another voice than mine and Phil's on this. The module bin feature should really just 'work' without the Wave provisos.

&gt; The module bin feature should really just 'work' without the Wave provisos.
Completely agree, I don't understand why it doesn't... I wrote a couple of modules in our nf-core-style modules repo that use module binaries, and I really don't love the restrictions it adds.

I should probably be evangelising for Wave as a Seqeran, and it is awesome, but it shouldn't be required for a language feature IMO

BTW, the softwareVersionsToYAML function from nf-core-utils plugin does handle a mix of versions.yml and topics version