search

nf-core / differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
https://nf-co.re/differentialabundance
MIT License
64 stars 37 forks source link

add module DESEQ2 #322

Closed suzannejin closed 1 week ago

suzannejin commented 4 weeks ago
LucilleAugusta commented 3 weeks ago

Hi @suzannejin,

I would like to work on this issue. Is the experimental branch created - or should I create one from dev?

Br, Lucille

suzannejin commented 3 weeks ago

hello @LucilleAugusta

Thank you for joining! We have a branch called dev-ratio, to which you should PR your changes.

You could see from this branch that we are trying to reorganize the structure of the pipeline into a more modular one. So that differentialabundance.nf calls --> subworkflow/experimental.nf And from this experimental.nf it calls to the subsequence analysis wrapped into subworkflows, basically: 1) subworkflow/differential 2) subworkflow/correlation 3) subworkflow/enrichment

You could add the DESEQ2 module into subworkflow/differential.nf

NOTE: as you may see, it is half added, in the sense we added at some point the call to DESEQ2, but then we updated the rest of the code, so it is not properly working. You would need to properly handled the input channels and call DESEQ2