Hi everyone, I have run the rnaseq pipeline on a couple of datasets. Firstly, thank you for the work you have already put in. This pipeline is very well designed, and it has significantly simplified my workflow. I mainly ran it to support colleagues’ exploratory work. I’ve always found it a bit frustrating to reach the DESeq part, defining all the theoretical comparisons, only to wait for R to loop through everything. To address this, I’ve created a subworkflow that uses a metadata sheet to generate all comparisons and then runs them. I’d like to potentially integrate my subworkflow into the overall rnaseq pipeline and contribute a little to its development. But I saw that there’s already a closed PR request for something similar (https://github.com/nf-core/rnaseq/issues/409), and the conclusion is that this wouldn’t be implemented directly in the rnaseq pipeline. May I ask if this is still the case?

Yes, there's a separate workflow for analysis downstream of rnaseq (#C045UNCS5R9). It does DESeq2, Limma, and other more advanced methods. There are no plans to extend rnaseq into that space, it's already a bit of a monster.

Ah, I see. I missed the new pipeline. Good to not replicate the effort then. Thank you

Added a comment to that (very old) issue for future googlers 👍🏻