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nf-core / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
https://nf-co.re/quantms
MIT License
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Move most modules from local into nf-core #63

Closed jpfeuffer closed 7 months ago

jpfeuffer commented 2 years ago

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 commented 2 years ago

FYI I'm working on moving the IDFilter: https://github.com/nf-core/modules/issues/2205

jpfeuffer commented 2 years ago

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

rolivella commented 2 years ago

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 commented 2 years ago

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 commented 11 months ago

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

jonasscheid commented 11 months ago

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 commented 7 months ago

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