Do you love nextflow and love telling other people that you love nextflow? 😅 nextflow zoom Maybe you should sign up to be an ambassador! Next round of applications is now open 🎉

Hello all! We have repurposed the old #request-upload channel, now renamed to #C09H6NYHR9T This channel will be used to track all the requests that need an action form a core team member, and you have dedicated Slack workflows to fill up a form and make your request, please use these! The available requests are: 📦 Uploading containers to nf-core quay.io 🪣 Uploading test-data to nf-core AWS S3 bucket 📄 Activating Zenodo links 📁 Transfer a pipeline repository to nf-core

📆 Welcome to 2026 everyone 📆 Following in the trend for many online communities, we are kicking off our announcements with a statement from the core team about the usage of AI and LLMs within the nf-core community! TL;DR: nf-core’s policy remains unchanged. If a pigeon were to commit good code, I would accept it. Humans are still ultimately responsible for their submitted code. We will not ban or restrict the use of AIs or LLMs as they can be useful tools for some people, if used appropriately. See the blog post for the full thing: https://nf-co.re/blog/2026/statement-on-ai Note that of course such a stance is not static, and we will adapt and evolve over time with the feedback from the community, so please feel free to open discussions with the community when you need!

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Hi folks! Remember that blog post we did about adopting new Nextflow syntax? Well, 2026 is the year of actually doing all these changes 💪🏻 🚀 nextflow It'll be worth it, I promise! First up was using topics in modules, which had a big effort during the Nextflow Summit Barcelona hackathon and is making great progress 🎉 (see #C09LJTQQ3EY) Second is making all pipelines compatible with the new Nextflow "strict syntax". This is backwards compatible across versions, but getting a green tick mark for it now means that your pipeline won't break when new Nextflow versions are released and the Nextflow v2 syntax parser becomes the default (v. likely in 26.04). To help with meeting this goal, I put together a little helper repo: https://github.com/nf-core/strict-syntax-health • Runs twice a day to keep stats of how many pipelines, subworkflows and modules are passing

nextflow lint

• Keeps copies of lint results, so you can click straight through to your pipeline without running anything The good news is that ~94% of both #CJRH30T6V and #C03D38JNFNJ are already passing 🎉 The less good news is that only 12% of pipelines are passing 🫠 So - please go see if your favourite pipeline is on the naughty or nice list, and let's see if we can get green ticks across the board in the coming weeks! ✅✅✅✅🎉 catjam neon cat spin nextflow shake ▶️ https://github.com/nf-core/strict-syntax-health ◀️ nextflow pet

Hi <!channel>! Our next hackathon is coming up! 👉 https://nf-co.re/events/2026/hackathon-march-2026 nf core shake 📆 • March 11-13, 2026 • Online / local distributed sites This year, we are using a hybrid format, with in-person hubs around the world and supported online participation. 📋 PROJECTS One new thing is that projects will be designated for either a primary specific in-person hub OR fully online. • This means project leaders will be present at their designated location. If you're at a hub, join an existing project or create one for your site! • Online projects will be supported by online group leaders. If you're joining remotely, pick an online project or create one of your own. 📌 LOCAL HUBS For the distributed hubs to work, WE NEED YOU! If you're able to book a meeting room or any other kind of space and host a local site, please head to the above page and submit a PR to register your hub. You can find instructions on how to register your in-person hub in the Hackathon website. • You don't need to have anything booked yet; it just helps us know who's interested. • Seqera will support hosts with overall coordination, communication, and snacks, so you won’t be doing this alone. Local sites can be any size. Previously, we've had anywhere from 4-80 people at a given site. Even if it's just you and a few colleagues, please do let us know! 📆 KEY DATES • Project proposals: Open NOW • Site registration: Open NOW • Participant registration: Opens February 2026 Please get those sites and projects registered ASAP so we can include them on the site. As ever, time is of the essence! calendar fire fine ⏲️ Drop any questions into #C0ACF0TPF5E!

The hackathon registration is now open: https://nf-co.re/events/2026/hackathon-march-2026#registration 🚀

Hi <!channel> 🚨 With the next major release of Nextflow comes strict syntax, which will cause pipelines to fail if the code is not compliant. We got you covered, but we need your help for the configs repo (https://github.com/nf-core/configs). 📣 Please check ALL institutional configs you use (whether within nf-core/configs, or in your own custom repositories) and see if they will still work with the new syntax parser! 👀 To help you do this, @James Fellows Yates and I wrote a blog post to hopefully make testing and fixing your configs super easy. You can find the blog post here: https://nf-co.re/blog/2026/configs-strict-syntax ⚠️ All configs in the nf-core configs repository that are not strict syntax compatible by the release of the next major Nextflow version will be marked as deprecated, meaning these configs are not guaranteed to work with all pipelines from that moment on. ⚠️ Feel free to come ask us for help or to have a chat about configs in #CGRTMASKY.

<!here> It's nf-core hackathon quiz time! https://uu-se.zoom.us/j/62398697184 - everyone welcome! (Even if you're not attending the hackathon!)

Hi <!channel>! I'm pretty excited to launch two new projects today: RustQC 🦀 🧬 and rewrites.bio 🚀

👉🏻 TLDR: I'm trying to get this to go viral on HackerNews! Please give us a helping hand if you like what you see! 😆 hacker news https://news.ycombinator.com/item?id=47616595

This story started about a month ago, when I jokingly said (not for the first time) that I should just rewrite dupRadar in Rust after seeing it break some #CE8SSJV3N runs again. I kicked off Claude together with Seqera AI, and this time it… worked! Fast forward a weekend’s worth of building, then several weeks of validation and incremental fixes, and #C0AQYAFSSV7 was born. It replaces the entire #CE8SSJV3N QC subworkflow (dupRadar, featureCounts, 8 RSeQC modules, preseq, samtools stats, and Qualimap) - which together account for over 15 hours of run time. RustQC finishes in around 15 minutes, over 60x faster. I’ve designed RustQC to be a drop-in replacement for those tools, so it’s totally optional. Output files are near-identical, so MultiQC works out of the box. There’s a dedicated Nextflow validation pipeline that uses #C049MBCEW06 to compare outputs against the upstream tools to ensure parity. I released it on Bioconda earlier this afternoon and@Jonathan Manning is quick off the mark, there's already a PR to #CJRH30T6V to add it (a PR to #CE8SSJV3N shouldn't be far behind). What’s interesting is that my Rust rewrite story is far from unique. Three days into my effort, @Rob Patro independently published about doing the same thing with piscem. Then @Nils Homer at Fulcrum just released fgumi earlier this week.. Something has clearly shifted. I’m both extremely excited and a little bit terrified at what I expect to be a wave of tool rewrites in bioinformatics. After a lot of discussion, we decided that these AI-assisted rewrites are coming whether we like it or not. The best thing we can do is to try to get ahead of them and establish some best practices to avoid what we see as the worst risks. To that end, we are also announcing https://rewrites.bio - a set of best practice guidelines for anyone else wanting to use AI to improve on bioinformatics tooling. It’s common sense stuff: Credit the original authors, emulate output exactly, don't file AI-generated bug reports, that kind of thing. Hopefully it starts a discussion around this topic for some community consensus. Anyway - I hope folks like what we’ve made. Looking forward to the discussion that comes around it 😀 • hacker news Hacker News post! https://news.ycombinator.com/item?id=47616595 • seqera RustQC blog: https://seqera.io/blog/rustqc/ • seqera rewrites.bio blog: https://seqera.io/blog/rewrites-bio/ • https://rewrites.bio • https://seqeralabs.github.io/RustQC/

Hi <!channel>! We are pleased to share the release of nf-core docs version 2 🎉 Documentation has been a known pain point for our community, and rather than patching things up incrementally, we decided to rebuild from scratch. Pages are more focused and purposeful, with content organised to guide you whether you're running your first pipeline or diving deep into development and contribution. Read the blog or explore the new docs for yourself 👉 https://nf-co.re/docs/

If you find some dead links because of missing redirects, please post them on #CE7DN1U7M or make an issue in the website repository

Do you work on virus bioinformatics? nf-core is co-organising with the VirJenDB team a hybrid satellite hackathon (online and in Vilinus 🇱🇹) on May 17th: https://evbc.uni-jena.de/events/vibiom2026/hackathon-satellite-event/ ⌛ The registration of interest form closes end of this week (April 17th) Current project ideas include: • virus biohazard contributing to VirJenDB, • bioconda adding tools to bioconda • nf core making virus-related nf-core modules • nextflow converting a bash workflow to Nextflow But you are welcome to propose any other project ideas (nf-core related or not!)!

Hi <!channel>! 👋 We’ve put together a short survey to better understand your experience during the nf-core Hackathon that took place in March. Your feedback will help us improve future hackathons—what worked well, what didn’t, and what we can do differently next time. It should only take a few minutes to complete. 👉 https://seqera.typeform.com/mar26hacksurvey Thanks in advance for your time and for being part of the hackathon! 🚀

Registration now open for the free live-stream of the Boston Nextflow Summit! 🎉 https://nfcore.slack.com/archives/C01G2VA2ZSP/p1776684103293579

Hi <!channel>! ✨ The nf-core core team just got bigger, and we couldn’t be more excited! Five amazing people who have been part of this community for a long time are now officially joining the core team 🥳 🎊 A huge welcome to: • @Anabella Trigila • @Arthur • @Louis Le Nézet • @Matthias De Smet • @Simon Pearce If you’ve ever had your PR reviewed, your question answered, or your hackathon snack eaten 🍕… There’s a good chance one of them was involved. We’re thrilled to make it official! 🙌 Want to know more? Check out the blog post 👇 🔗 https://nf-co.re/blog/2026/new-core-members

After some hiccups we will now roll-out nf-core/tools 4.0.2 🎉 🐍 Why the major version bump? We switched the template to require strict Nextflow syntax. More highlights: • Auto-generated container config files (more on that soon) • New command aliases • Webhook notifications replaced with Nextflow plugins -> slimmer template You can read more about these and further changes (e.g. faster pre-commit hooks 🦀) and also how to solve common merge conflicts in release the blogpost: https://nf-co.re/blog/2026/tools-4_0_0 (a video with a code walkthrough will come soon) If you need help or find bugs, feel free to drop a message in #CE5LG7WMB

Many thanks to everyone who attended the Boston Nextflow Summit and nf-core hackathon! We've just got the official photos online, they're great 📸 🎉

Are you seeing type mismatches after updating to Nextflow v26.04.0? Or do you want to ensure your pipeline is fully compatible with strict syntax? Then this blog post will be an interesting read for you! https://nf-co.re/blog/2026/parameter-types

<!channel> registration is now open for the next nf-core hackathon! There's a discount if you register soon, so there's no time to waste! Hope to see many of you in Barcelona, it should be a really fun event 🎉 Registration is also open for the online (free) summit talks!

Hi <!here>! Heads up that the early-bird 25% discount for the Barcelona hackathon 🇪🇸 runs out at the end of July, so get those registrations in quickly! Also, the call for abstracts for the online/virtual Summit is open only for a few more days! Get your talks in now! 🎤 nextflow bounce

We recently found a bug in the pipeline template (primarily since template version 3.0.0) that allowed the read-out of the nf-core-bot token. We therefore are currently rolling out patch PRs to all nf-core pipelines. See the security advisory for details and what pipeline maintainers have to do to mitigate it: https://nf-co.re/advisories/pr-comment-workflow-vulnerability deal with infra

This only affects nf-core pipelines, and not pipelines using the template that are outside of nf-core - unless you've set up your own token/bot (as the nf-core bot only works within the GitHub organisation). This is a precaution only, we don't have any evidence that anything bad is happened, we're just trying to be proactive. Thanks all!

We released nf-core/tools 4.1.0 today 🎉 Main highlights: •

nf-core modules container create

takes care of all the things containers in modules (reads the

environments.yml

to build a seqera container using wave wave containers in all the flavors of the rainbow (singularity, docker, amd64, arm64) + conda lock files and updates the main.nf and meta.yml with the correct info) 🚢 •

nf-core modules bump-version

uses the above to bump the version and build the new container and updates them in the main.nf in one go 🆙 • ~7x faster CLI startup. finally

nf-core modules --help

feels almost instant again (similar improvements for most commands) sonic The main focus of this release was on the CLI, so the pipeline template updates are not so big this time (🤞🏻), mainly version updates and typo fixes. We are still testing them, so we will roll out the sync PRs at a later time. Read more about this including some performance improvement graphs in the release blog post: https://nf-co.re/blog/2026/tools-4_1_0 Have fun building containers!

Only 2 weeks left to register for the Barcelona hackathon! https://nfcore.slack.com/archives/C01G2VA2ZSP/p1788853215207279 If you've been on the fence or thinking about it, now's the time to get those registrations in 🙂 Some great projects already, and places have been filling up fast. Join us for a few days of building nf core scroll (psst: also, there will be new exclusive stickers and swag, just saying 👀 )

Last chance to register folks! Go go go! https://nfcore.slack.com/archives/C01G2VA2ZSP/p1790149807256409

We recently found two more possibilities for keys to be leaked in the pipeline template, similar to the previous one, but this time the fix is a bit easier (just one patch PR per repo) and we also kicked off centralizing the nf-core actions https://github.com/nf-core/actions You can find out more in the two security advisories: https://nf-co.re/advisories/fix-linting-workflow-vulnerability/ and https://nf-co.re/advisories/aws-test-debug-log-secrets/

⚠️ Announcement for all community members in the nf-core GitHub organisation ⚠️ We will be activating the requirement for two-factor authentication (2FA) for all members of our GitHub organisation! 🔒 To improve our security, we will be bringing our GitHub organisation in line with current best-practices. 📈 Currently 75% of our members in the GitHub organisation have 2FA, but around 400 people do not. What this means for you: 1. Not in our GitHub organisation: nothing! Please disregard this message. 2. In our GitHub organisation and 2FA activated: nothing! Please disregard this message. 3. In our GitHub organisation and 2FA is not activated: ◦ Please turn on your preferred 2FA method ASAP (docs: https://docs.github.com/en/authentication/securing-your-account-with-two-factor-authentication-2fa/configuring-two-factor-authentication) ◦ If you do not: you will not be removed from the organisation. However you will no longer have permissions to commit or contribute to GitHub repositories under the nf-core organisation. ◦ Deadline: 30th October 4. An outside collaborator to an nf-core GitHub repository and 2FA is not activated: ◦ Please turn on your preferred 2FA method ASAP (docs: https://docs.github.com/en/authentication/securing-your-account-with-two-factor-authentication-2fa/configuring-two-factor-authentication) ◦ Please join the nf-core GitHub organisation via #CEB982K2T ◦ If you do not: you WILL be removed from all nf-core repositories ◦ Deadline: 30th October If you have an issues or problems, please post on #CE6SDBX2A and a core team member can help you.

Thank you everyone for being part of an incredible week last week, with summit, hackathon, training and more! nextflow bounce nf core scroll nf core socks If your FOMO wasn't strong enough and you're curious to see what we all got up to in Barcelona, you can see the photos here: https://nfcore.slack.com/archives/C0BKZMG6467/p1792495983801029 Summit talk video editing will now commence and will be available on YouTube in a few weeks. If you want to get started early, you can still register for the virtual summit and watch all the sessions in the event platform: summit.nextflow.io/2026/virtual/overview