🚀 Seqera Co-Scientist is available for the hackathon! 🚀 Hi everyone! 👋 To help you during the hackathon, we've added credits to the

nf-core_events

organization on Seqera Cloud and added all Hackathon participants to it. That means you can use Seqera Co-Scientist, our AI assistant for Nextflow, nf-core and Seqera Platform, at no cost to you. What can it help with? • Writing and debugging Nextflow code (including strict syntax fixes, configs and

nextflow_schema.json

) • Finding nf-core modules and showing you how to run them • Understanding how an existing pipeline is put together • Building containers with Wave (e.g. "Create a container with samtools and bwa from bioconda") • Writing nf-tests and fixing failing ones • Launching and debugging runs on Seqera Platform 1️⃣ Install the CLI You need Node.js 18+ on macOS, Linux or Windows (WSL).

npm install -g seqera
seqera --version

Getting

seqera: command not found

? Make sure your npm global bin folder is on your

PATH

. Getting permission errors? Run

npm install -g seqera --prefix ~/.npm-global

, then

export PATH="$HOME/.npm-global/bin:$PATH"

. 2️⃣ Log in

seqera login

A browser window opens where you sign in with your Seqera Cloud account. If it doesn't open, copy the URL from your terminal into your browser. 3️⃣ ⚠️ Pick the

nf-core_events

org (important!) Co-Scientist bills usage to whichever organization you have selected. If you belong to more than one org, make sure

nf-core_events

is the active one, or the hackathon credits won't be used:

seqera org            # shows your current org
seqera org switch     # choose nf-core_events

4️⃣ Start Co-Scientist Start it from inside your pipeline's folder so it can see your files:

cd /path/to/your/pipeline
seqera ai

Handy tips •

/help

, or just type

/

, to see the built-in commands and skills • Shift+Tab switches between build mode (makes changes) and plan mode (read-only analysis and planning) •

/goal <task>

keeps it working on a longer task, e.g.

/goal add nf-tests for the new module

•

/status

shows who you're logged in as and which org is active •

/credits

shows the org's credit balance and your usage •

seqera ai -c

picks up your last session where you left off • It asks for your approval before it runs risky commands or changes files outside your working directory Some prompts to try > Show me the structure of main.nf > Find nf-core modules for variant calling > Why is my pipeline failing? > Help me write an nf-test for this module Already using Claude Code, Codex or Copilot? You can add Co-Scientist to them as a skill with

seqera skill install

. 📚 Docs: docs.seqera.io/platform-cloud/seqera-ai/get-started Questions or problems? Ask in this thread. Happy hacking! 🎉

https://nationalgnomicsinfrastructure.github.io/ 🌵🟢🌍🔬

don't forget to run

prek install -f

after you cloned a nf-core repo, to get all linting run automatically

This isn't worth making a dedicated project but if anybody wants to look at a nextflow GUI launcher (targeting nf-core) feedback would be great https://github.com/ARTIC-Kraemer-Lab/GLACIER

it's designed for helping non bioinformatics specialists to make effective use of nextflow pipes

Hello there! If you have a run with lineage on, give it a try on the codespace of the repo and tell me whether it makes any sense for your pipeline. github.com/QuietFlare/clew I’m at table in the front, please come by if it breaks or if you just want to see it run. Thank you 🙂

anyone else getting rate limited?

Caused by:
    Wave invalid response: POST <https://wave.seqera.io/v1alpha2/container> [429] {"message":"Request exceeded build rate limit for IP 83.51.254.156"}

Hi, as a side activity while migrating the pipeline to a new template, I've created a scripted migration tool: github.com/Skitionek/nf-migrate Validated it against handmade migrations performed in a bunch of repos: github.com/Skitionek/nf-migrate/blob/…/validation.md It seems that 80% of manual groundwork can be cut off - leaving the final 20% for AI to polish off! 🤖✨

Project leads, attention! alert <!channel> We'll have the wrap-up of the first day at 16h30 so please make sure you have the wrap-up slides of your project ready by then 😉 docs.google.com/presentation/d/1tT_pGwbTZFU…/edit?usp=sharing

See that there was change of venue, anybody still here to share location?

Take a gander at latest messages in #C07ACNLELR2 for a taste of the discussion the static types/ meta pipelines group would like to put to you all this morning!

<!here> Sock hunt pictures here

<!channel> post your best scores in the 🧵 on hackerthon tycoon! There is a priiizzeeee!

First rubberduck has been award for the most sock stickers found in the sock hunt rubber ducknf core socks

Hi I just checked the organizations i am part of and i only have community Is there a chance i could be added to nf_core_events

Thank you all for a lovely event. Meeting and talking with everyone was the best part. Events like this are where you hear the real problems people are trying to solve, and I learned a lot from those conversations. Thanks to the organisers for such smooth, warm and funny two days. Sorry I had to head off early and miss the wrap-up. Hope to see you all at the next one!

💪

how can I install the Seqera plugin for copilot and claude?

For people interested in parsing the agentic modules stats we gathered, along with their actual PRs: docs.google.com/spreadsheets/d/14oPqv-WXwYX…/edit?gid=0#gid=0

Thanks everyone for your work this week! As a reminder, here are the slides recappping what we all did: docs.google.com/presentation/d/1tT_pGwbTZFU…/edit?usp=sharing

Anyone wanna grab some food soon?

<!here> if anyone wants to join for Pizza (here) at 8pm then comment on this thread, I will book a table.

I was chatting offline with @James Fellows Yates on naming standardization re: the epic hackathon record discussion. My very tangential thought was linkml.io , I have barely started to understand what it might be useful for, but thought to raise it to the group in case other people not have heard of it, and might find it useful for one thing or another.

I totally forgot. Somebody payed a bear for me yesterday. I don't know the name. Can the person please dm me 🙏!

For anyone who joined the discussion earlier today about nf-/nextflow-test feature ideas, I did a write-up here.

Photos from the nf-core Hackathon are here. Check out the gallery: summit.nextflow.io/2026/barcelona/gallery

<!channel> 👆🏻

Hi folks! We recorded the wrap-up talks on day1 (the audio quality is very bad sorry, but hopefully better than nothing). You can see them here: