# Contributing to Open-Source Bioinformatics: Our Experience at the nf-core Hackathon from Medellín > If you work anywhere near data-heavy science — genomics, metagenomics, proteomics — you’ve probably hit the same wall: building reliable, reproducible data pipelines is hard. Nextflow is an open-source workflow engine… - URL: https://lokahq.github.io/tech-blog/contributing-to-open-source-bioinformatics-our-experience-at-the-nf-core-hackathon-from-medellin/ - Type: Blog article - Authors: Andres Florian (Bioinformatics Engineer), Daniel Sabogal (Junior Bioengineer) - Published: 2026-07-09 - Updated: 2026-09-30 - Reading time: 4 min - Tags: Bioinformatics, Nextflow, Metagenomics, Hackathons - Originally published on Medium: https://medium.com/loka-engineering/contributing-to-open-source-bioinformatics-our-experience-at-the-nf-core-hackathon-from-medell%C3%ADn-64e83f254576 --- _Written by_ [Andres Florian](https://medium.com/@andres.florian) _and_ [Daniel Sabogal](https://medium.com/@daniel.sabogal_68144) ## What is nf-core, and why does it matter? If you work anywhere near data-heavy science — genomics, metagenomics, proteomics — you’ve probably hit the same wall: building reliable, reproducible data pipelines is hard. [Nextflow](https://www.nextflow.io/) is an open-source workflow engine designed to solve exactly that problem, letting scientists write scalable pipelines that run consistently across laptops, clusters, and cloud environments. [nf-core](https://nf-co.re/) is the community layer on top of Nextflow. It’s a collaborative project that curates high-quality, peer-reviewed pipelines and reusable modules — think of them as vetted building blocks that any researcher can plug into their own workflows. The result: less time reinventing the wheel, more time doing actual science. Twice a year, nf-core organizes a global hackathon where contributors from around the world gather — online and at local hubs — to build, improve, and ship these community resources. In March 2026, [the hackathon](https://nf-co.re/events/2026/hackathon-march-2026) brought together 29 hubs across 20 countries. Loka hosted two of those hubs: one in **Medellín, Colombia**, and another in **Skopje, North Macedonia**. ## Why Loka at an nf-core hackathon? Nextflow comes up regularly in our client work — in cloud migrations, proof-of-concept builds, and production-grade pipeline development — so contributing back to the open-source ecosystem felt like a natural step. This post covers the Medellín experience. ## The Medellín node: small team, focused mission Our hub operated out of a WeWork space in Medellín on March 11–12. Three of us worked a standard 9-to-5 with a clear goal: **create and publish new nf-core modules**. We scoped five modules and made strong progress on two, taking both to a publishable state within the two days, both of which were later merged into the official nf-core repository. ## Module 1: `stacks/refmap` — variant calling for ddRAD-seq data [Stacks](https://catchenlab.life.illinois.edu/stacks/) is a widely used software suite for analyzing restriction site–associated DNA sequencing (RAD-seq) data, a technique commonly used in conservation biology, population genetics, and ecological research. The `refmap` component performs reference-based variant calling from this type of sequencing data. During the hackathon we: - Refined the module’s process definition to meet nf-core standards. - Tested and validated Docker and Singularity containers, as well as the Conda environment definition. - Prepared the pull request against the official [nf-core/modules](https://github.com/nf-core/modules) repository. The module was essentially finished by end-of-day two. After the hackathon, a maintainer left some review comments; we addressed them, and the module was **successfully merged** into the official nf-core repository. You can find it live at [nf-co.re/modules/stacks\_refmap](https://nf-co.re/modules/stacks_refmap/). ## Module 2: `singlem/dbdownload`— taxonomy database for metagenomics [SingleM](https://github.com/wwood/singlem) is a tool for metagenomics taxonomy classification — it helps researchers figure out which organisms are present in a complex environmental sample. The module we worked on wraps its database-download functionality, allowing users to fetch the required taxonomic database directly within an nf-core pipeline. During the hackathon we: - Refined the process definition and environment configurations. - Fixed linting issues and completed all required nf-test tests. We finished the pull request shortly after the event, and this module was also **merged into the official nf-core repository**. You can find it live at [nf-co.re/modules/singlem\_dbdownload](https://nf-co.re/modules/singlem_dbdownload/). ## What we learned Beyond the code itself, the hackathon was a crash course in the nf-core ecosystem. Some highlights: - **nf-core module standards and best practices.** The project has thorough guidelines for everything from naming conventions to container specifications. Working within these constraints taught us a lot about building robust, community-ready bioinformatics resources. - **Testing with nf-test.** Writing meaningful tests for bioinformatics modules — where inputs and outputs are often large, domain-specific files — requires thoughtful test-data selection and snapshot strategies. - **The power of daily stand-ups.** Each day ended with an Americas-region wrap-up session ([Day 1](https://www.youtube.com/watch?v=tl--RcgMFNY) · [Day 2](https://www.youtube.com/watch?v=kHmzx0g2SIM)) where every hub shared progress. Seeing teams from Buenos Aires, Cambridge, and North Carolina working in parallel was genuinely motivating. ## What’s next We ran in parallel with Loka’s other hub in Skopje, a team of 20+ tackling larger-scale pipeline work: extending the existing [nf-core/proteinfold](https://nf-co.re/proteinfold/) pipeline with new tools for evaluating the accuracy of AI-based protein structure predictions, and building a brand-new antibody optimization pipeline. Two hubs, two very different scopes, same goal of giving back to the ecosystem. On our side, two merged modules is a strong start for a first outing, and we’re not done. We still have the rest of our scoped backlog and are continuing to work through it, with more PRs to [nf-core/modules](http://github.com/nf-core/modules) planned in the coming weeks. If you work with data-heavy science and have never contributed to open source, a hackathon is a low-risk way in: the standards are well documented, maintainers are responsive, and you walk away with merged work that the whole community uses. ![The Medellín node of the nf-core March 2026 hackathon — a small but determined team](https://lokahq.github.io/tech-blog/blog/contributing-to-open-source-bioinformatics-our-experience-at-the-nf-core-hackathon-from-medellin/1-ypDpr5EKNfI_zue5U69lQQ.webp) The Medellín node of the nf-core March 2026 hackathon — a small but determined team If you’re interested in contributing, keep an eye on [_nf-co.re/events_](http://nf-co.re/events) _for the next hackathon — they run twice a year._