it seems like the "aws results" tab is broken on several of the pipeline documentation pages? sometimes the "no aws results found" message appears as soon as i click on the tab and sometimes it takes digging into the folder structure and getting to a level where files should be

Can someone point me to documentation for adding a step to a pipeline? Specifically, I want to add a samtools index step so that both BAM and BAI files are output from the scrnaseq pipeline.

Hi there, is it possible to embed a YouTube video on the usage docs page of the pipeline docs to be also displayed on the website? We have a recording from an online nf-core/airrflow tutorial. This would be separate from the bitesize talk that is already embedded on the website, which explains what airrflow is useful for.

Hey all, I'm pretty new to using the NF-Core pipelines, and first and foremost, I wanted to say that they are phenomenal! I hope that everyone who has worked on them is very proud, as they represent incredible accomplishments! This has probably been suggested before, but I just wanted to mention an (admittedly rather involved) idea I had when it comes to documenting the outputs of the pipelines. Thanks to the user-friendly designs, I've found it easy to set up and run the pipelines, but given their increasing complexity, one often ends up with a ton of outputs that can be somewhat difficult to understand in relation to the overall pipeline. I was thinking that it would be helpful if the "Output" tab of the NF-Core pipeline documentation had a place where you could paste in the command you ran (potentially with the samplesheet too, as needed). Then, ideally, the platform would detect which settings you specified and know the defaults for the ones you didn't. Then, it would output a visualization of the pipeline that actually ran. One would then be able to hover over the steps in the visualization and see which outputs are expected for each. You could also click on those outputs to get detailed information explaining their contents. Here's a mock-up of this for a segment of the Airrflow pipeline. Obviously, creating something like this would be a ton of work, but since the Nextflow team doesn't appear to be daunted by ambitious undertakings, I figured I'd mention it.

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Hi all, I'm looking forward to the hackathon this week. I'm Jess and I'm a bioinformatician in the NHS. I have limited nextflow/nf-core experience (have converted a Python Ruffus pipeline into Nextflow and tried to do some nf-tests but got a bit stuck) but would like to get more experience in the future. My timezone is London GMT

Awesome 😄 Nice to have you on board @Jessica Kan! If you're in European timezone, then I will be leading that phase! I am online-only, so we will be joining on the WorkAdventure space and here :) We will follow the main hackathon schedule, however I'll be out for a brief appointment (probs 10-20m) at 10:00 CET (so 09:00 GMT) The goal of our project is: https://nf-co.re/events/2026/hackathon-march-2026 And the github project board for our group is: https://github.com/orgs/nf-core/projects/146/views/14?filterQuery=group%3ADocumentation&groupedBy%5BcolumnId%5D=258188611 So we can discuss issue allocation depending on preferences tomorrow 🙂

Hi all, my name is Meng, I recently completed my PhD in population genomics at the University of Toronto. I have used snakemake before but have limited experience with nextflow. I’m looking to get more experience with nextflow/nf-core through contributing to the v2 documentation project in this hackathon, and add new pipelines in the future. I’m gonna go over more training materials/examples for nextflow today to get ready for tomorrow. Looking forward to contributing and collaborating! My github handle is imengyuan and my timezone is Canada eastern time EDT

Hi my name is Peter. I am doing a PhD on hackathons and accessibility. I have a little experience with nextflow/nf-core. But hoping to learn more during this hackathon. My timezone is UK GMT.

I thought I’d get started but I made a mistake by directly committing to the doc-v2 branch rather than fork and PR, I have reverted the commit and submitted PR the correct way, sorry for the inconvenience! Please let me know if there’s anything else I should do if it’s not fixed properly, here are the links issue PR

No stress - a good reminder for us to add branch protection 😁

@James Fellows Yates - when you're online could you add something to stop merges to that branch?

👋 For anyone wanting to chat about the version 2 documentation for the hackathon, head on over to #C0AKTARC9D2

Hello everyone! I'm taking over from Chris now he's going to well-deserved rest! I will be on the hackathon workadventure (https://app.hackathon.nf-co.re) today in Room 6 (on the right hand side of the space). I will only be online until about 14:30 CET (13:00 GMT) because of kids related stuff, and I have a short appointment at 10:00 CET - so if you arrive and I'm not there sorry about that but check over at #C0AKTARC9D2 as there will be instructions there 🙂. Otherwise hopefully this morning we can get some others trained up, and maybe they can help 'onboard' people from the Americas 🙂

PR fixing a lot of links across

docs-v2

branch

And finishing overhaulling the meta map page: https://github.com/nf-core/website/pull/4057

Nice! There should be a link checker we can run 🤔

You will see I started a PR to mop up open issues

So we're super close to merge (after redirects)

Nice! There should be a link checker we can run 🤔

I think we used to have one (right @mashehu?) but it was turned off because it was slow or broke a lot... I think?

In the meantime, another minor PR after I couldn't intuitively find the page I was looking for when working on a PR for createtaxdb: https://github.com/nf-core/website/pull/4078

(moving a page essentially, with an alternative suggestion if you prefer)

A page I really need right now has vanished: https://nf-co.re/docs/tutorials/migrate_to_strict_syntax/config_strict_syntax

I am praying to the docs and infrastructure gods, goddesses, elves, fairies, unicorns, magical entities, good or bad. Please help 🙏

I assume we dropped https://docs-archive--nf-core-docs.netlify.app/docs/tutorials/nf-core_training/writing-nf-core-modules/chapter-1-introduction (see https://github.com/nf-core/website/issues/4145)?

any one can help me understand how to determine the --mendaka_model to use in genomeassembler pipeline? thank you

Hey! Where should I report documentation issues?

@mashehu feel free to ping docs team on stuff like this too: https://github.com/nf-core/website/pull/4488#pullrequestreview-5636737013 But as a general thing, what is the procedure about package locks and how is one meant to resolve the conflicts?