Move most modules from local into nf-core

[jpfeuffer]

Description of feature

Especially the ones from the openms/subfolder. So they can be reused for other pipelines.
They should be mostly nf-core compatible already but might require some tests and minor adaptions.

[rolivella]

FYI I'm working on moving the IDFilter: nf-core/modules#2205

[jpfeuffer]

That's great. Having the first example hopefully will help other contributors to help out.

[rolivella]

Yes! But I think is not intrinsically related to quantms pipeline. nf-core modules are not linked to this pipeline, are general modules that can be reused into any pipeline...

And It's going to take me some time, is quite complex! I'll not finish it today in the hackathon.

[jpfeuffer]

Yes true, the first step is to make nf-core modules (e.g., out of the ones in quantms), which is a "global" nf-core task. Then we can start replacing the local ones here with the global ones.

[jonasscheid]

FYI: https://nf-co.re/modules/openms_idfilter

[jonasscheid]

And I had the time to do some more (simple) modules during the last hackathon 🥳
https://github.com/nf-core/modules/tree/master/modules/nf-core/openms

[ypriverol]

This is a major refactoring. I will close the issue for now.