A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

This pipeline would definitely benefit from some maintenance work :100: <@U0BG66J533K> - if you're willing and able to help that would be great! The beauty of nf-core is that anyone can jump in and work on pipelines.

This pipeline was originally built by <@UH3TTFNRJ>, but more recently <@U08UJCD6E0Z> has been doing some work by the look of it.

It'd be great if the two of you could work together to push the pipeline forward and get it up to date!

Yes, I really want to get into fixing the bugs, but mainly the latest nextflow parser update makes it even unable to run this pipeline. Once I get that fixed from my side, I will surely do my contributions.

I would also like to know is it ok to merge the contents the nf-bot is PRing

the template updates generally need some merge conflicts resolving, but other than that, yes, you can merge them

And if you need reviews for your PRs then please ask on <#CQY2U5QU9>, especially note that you're working on an abandoned pipeline :wink:

For template PRs, see the docs: <https://nf-co.re/docs/developing/template-syncs/overview|nf-co.re/docs/developing/template-syncs/overview>

Also if you're curious, I have a <https://nf-co.re/hackathon-projects/hackathon-barcelona-2026/ai-template-updates|hackathon project> in a couple of weeks where I want to look into how to make this process easier for folks with LLMs.

I've been trying to collect tips and tricks from folks in <https://github.com/nf-core/agents/issues/12|this issue> for that purpose. Might also be useful for you here.

I have a bit of interest with this one, too, shout out if you need help

Thank you for the overwhelming support and replies. I will try to do my best of support to this repo. Our lab is thinking of using this template for an upcoming HiC research. So, I am testing this out, just before. I will do as much help as I can.

I would like help on <https://github.com/nf-core/hic/pull/245|github.com/nf-core/hic/pull/245>, I have made some changes. I am skeptic about the docker checks. They are using the old template it seems. Can someone help me on that <@UE6D8290F>

Can you run `nf-test test tests/ --update-snapshot --profile docker`  (or singularity or conda, depending on which you use).
Something weird is going on with the first snapshot, where it seems to have captured a bunch of the stdout when it shouldn't have.
Both snapshots have a change to the md5sum of `SRR4292758.1000_balanced_insulation.tsv` , which might just need excluding from the md5sum check and just capture the name, depending on why