Hi @pierre-francois.roux, I really like the pipeline steps you proposed (for others interested check the proposal here: github.com/nf-core/proposals/issues/153). However, I think it could also be a very nice extension to the current atacseq pipeline. To get the discussion going and potentially find a common ground 🙂 I see two potential routes: A) Would it be fine for you to implement the proposed analyses steps in the current pipeline? • We would need to see what Jose will say. • I wouldn't mind to get involved here as well / review things when needed. B) Would you want to develop an independent downstream analysis pipeline? - • It could be similar to the scdownsteam pipeline. • Here I see more overhead for you and the atacseq pipeline devs to get things compatible and in sync. • In case you prefer this, I think it would be good to clarify which files you would need as inputs for such a downstream pipeline and redefine your proposal to minimize overlap with the existing atacseq pipeline. What do you think? Cheers, Kevin