Hi! I registered for hackathon 2026 and have some ideas what to add into your pipeline. Some of my friends (we are online team of 7 people) already wrote them in some chats, but I want to discuss some of my thoughts here, if it is ok! 1) What do you think of implementing optional inferCNV (which is vital when analysing cancer data) and cellphonedb (for ligand-receptor communications analysis). 2) I see there was an idea to implement gene regulation step. If it is still in demand, that would be interesting also https://github.com/nf-core/scdownstream/issues/119 3) I just wondered, did you think to add a step for some gene set enrichment analysis (ssgsea, aucell, etc)? Thank you!

Hey👋 amazing to have so many people interested - make sure to leave some github stars⭐ Quick overview of your proposals: • inferCNV sounds good • cellphonedb: the pipeline already has LIANA, which includes cellphonedb, so I think this is rather a no • Gene regulation: Generally yes, there have been two people that were interested in this at the barcelona hackathon 1.5 years ago, but they never finished the implementation. You can look at their branches, I think they still exist. However I am not an expert on this, and I would like to know in more detail what you are exactly planning if you approach this • GSEA: yes, fully open to these, just let me know in more detail what you are planning In general it would be amazing if you could first write a brief overview of what you are planning to add and where you want to add it to the pipeline, just so I can give feedback before you put too much effort into it

@Nico Trummer Thank you for reviewing the ideas! We will discuss it with team tommorow morning, and then will go in this thread. Maybe it would be convenient to discuss some of these in the virtual room within nf-core hack space with you or other person in-charge for contributing to your pipeline! I still don't quite understand, how the participation in hackathon works. Am I right in understanding, that after an approval of a plan, we can just start implementing some of these changes?

Well, usually I (as the primary maintainer of #C077PUX8DBP) would overlook the implementations, check in regularly with everyone working on 'my' pipeline and making sure everything is on track Now the problem is I am currently doing an internship that is not at all related to this pipeline, and I will have to work during the hackathon time. Thus, I can only give limited guidance during the hackathon. For this reason, I did not create a hackathon project on #C077PUX8DBP myself. However, there seems to be quite some people interested in contributing, so I will do my best to allow you guys to learn, and also to contribute something meaningful. Besides you, there is the guys who signed up this hackathon project. I am not sure if you are in touch with those anyway, but it would be important that we all keep in touch closely during the hackathon. The hackathon in general is not competitive, it should be an environment that allows newcomers to learn how to write proper nf-core code, and also the maintainers to offload some tasks that have been in the backlog for way too long. I am not sure yet how we can distribute tasks, but we will work something out. During the hackathon, everyone will work on their task (can also be in small groups) and try to figure out how it needs to be done properly. You can use #C077PUX8DBP (for pipeline-specific questions), #CE6SDBX2A and #C043FMKUNLB (for general nextflow/nf-core questions) and I think also the digital space that is provided for the hackathon (I am not sure how it works exactly, but I think something like this is planned) for asking questions. The goal is for you to open pull requests, which I will then review and - in the best case - merge into production

@Nico Trummer hello, no, our team (which includes @Gleb Khegai) is completely online, we are not related to Istanbul offline team, but one of us is already in touch with them (namely with @Emre Cevik and @Kurayi). Hope no double work will happen! But to ensure this I guess it's best to leverage GitHub Project feature (there's dedicated hackathon project), so we can assign tasks to ourselves. But as for now no #C077PUX8DBP repo related tasks can be found there :( I mean not new ideas proposed by @Gleb Khegai (yet) but issues from repo's backlog. Hope they will be added soon!

Okay amazing. Then please populate this tomorrow, I think you can just assign the issues from the #C077PUX8DBP repo to the corresponding project - there should not be any special permissions required for this Feel free to ping me on github or slack at any time, I can not promise I will respond instantly (as I will be working), but I will try to respond within 2h max.

Thank you @Nico Trummer for your quick response and dedication to guide us despite your packed schedule! I'll check if I can put tasks into GitHub Project. Will be also waiting for @Gleb Khegai to elaborate on GSEA idea. Maybe it's worth to repeat your last messages in a separate message in #C077PUX8DBP and/or #C0ACF0TPF5E?

I will send an explanatory message to the #C077PUX8DBP channel tomorrow morning, too tired today for writing something that suits the occasion

@Nico Trummer I've managed to put the issue into hackathon project, so you can recommend others to do this too with new and existing issues for better coordination between the teams and single participants as well