Welcome

Join us in person for the October 2024 nf-core hackathon!

This hackathon will be held in advance of the Nextflow Summit 2024 in Barcelona, Spain and is organised jointly.

Nextflow Summit 2024 - Barcelona

How the hackathon works

What to expect

The nf-core hackathons are collaborative, community-driven events where participants work together on projects.

Everyone is welcome, no prior experience of nf-core contributions is needed. However, we do expect that you have some experience with writing Nextflow code. Note that there is a separate training event for learning Nextflow and nf-core from scratch, running in parallel to the hackathon.

nf-core hackathons are not just about coding! We also have a lot of fun. We typically run things like a quiz, a bingo and have several small prizes for the winners. In addition to small social games and contests during the event, we also have a social evening.

Prerequisites

Before you arrive at the hackathon, please make sure that you have:

Where to find tasks

We collect all tasks in the “Hackathon October 2024” GitHub project board.

If you are not too familiar yet with the code base, a great starting point is to filter for issues labelled as good first issue.

Once you found something, get in touch with the project group (i.e. ping them on slack, find them in the room), assign yourself, and get started.

How to contribute code

We use GitHub to collaborate on code:

  1. Find a hackathon project
  2. Discuss with the group and assign yourself to an issue. (Create one if it is not there)
  3. Fork the repository
  4. Work on a branch in your Fork
  5. Once ready, open a PR to the parent repository
Note

Only assign yourself to an issue if you are ready to work on it, typically one issue at a time.

See Helpful resources below for more information.

Schedule

The hackathon will run from Monday 28th October to Wednesday 30th October. The registration opens on Monday at 9am. We will start at 10am everyday and close at 5pm on Monday and Tuesday. On Wednesday we will wrap up at 1pm. For a complete schedule visit the summit agenda page

Projects

This hackathon we will use projects, as opposed to the broader groups of previous events. At the end of each day, we will group the projects into categories and sum up their progress. Projects can be anything from:

  • Adding new features to existing pipelines
  • Adding and improving nf-core/modules
  • Improving the website and nf-core tooling
  • Creating entirely new pipelines
  • Discussion and planning community initiatives
  • Working on special interest group topics
  • …anything else

You can bring your own favourite topic or choose from a list of open issues in the community. Each project has a lead who can point you in the right direction.

You don’t need to commit to a single project and are free to move around groups and projects throughout the event.

Submit a new project

New projects can be proposed in the #hackathon-oct-2024 slack channel. Use the project proposal form to submit an idea. After a some community discussion, you can add your project to the list below and others can find it.

Tip

If you are planning to start a new pipeline, please propose it on the #new-pipelines slack channel ahead of the hackathon start to avoid delays during the event.

Once a project is approved, the project leaders should add it to this webpage and add issues issues to the GitHub project board ahead of the hackathon. If appropriate, label them as good first issue.

Join a project

Joining a project is as simple as turning up and getting in touch with the group. If you don’t know where to find them in the room, ping the project lead on slack.

You can move freely between projects throughout the event.

Overview of all projects

Regulatory

This group will work on tasks for the #regulatory special interest group. Most likely we will try to come up with more detailed plans on how to tackle different needs of subgroups within regulatory and try to come up with a strategy on how to both align between those subgroups as well as to come up with plans / proposals for the wider community what we could add to enable e.g. auditors or authorities to understand better what nf-core already provides.

Goal: Clearing out the scope of the regulatory special interest group and discussing who would tackle different subfields of the entire regulatory space for future improvements on nf-core guidelines and pipelines.

Group Leaders

Github user apeltzer
Alexander Peltzer

References

Continuing the discussion from last year’s hackathon, this group will work on tasks related to references’ genomes handling / management. Some work has started with nf-core/references but it is at a very early stage. This hackathon group will work towards agreeing on a fundamental structure and plan.

Goal: Replacing iGenomes, then world domination.

Group Leaders

Github user maxulysse
Maxime Garcia
Github user pinin4fjords
Jonathan Manning

Tube map polishing

Details coming soon

Goal: coming soon

Group Leaders

Github user mashehu
Matthias Hörtenhuber

nf-test plugins

nf-test is a very important piece of our modules, used for continuous integration testing of all our modules. However, writing tests for some file types / more advanced tests can be difficult. In this group we will try and kickstart the creation of nf-test plugins to make our testing a lot easier. This will mainly involve the development of nft-utils, the improvement of nft-bam and hopefully the creation of completely new nf-test plugins.

Goal: Fully develop nft-utils and start new nf-test plugins

Group Leaders

Github user nvnieuwk
Nicolas Vannieuwkerke

nf-core/seqinspector

nf-core/seqinspector aims to be a pipeline for initial quality control of sequencing data. Input is either FASTQ files or a run folder, and output is planned to be a global MultiQC report and, if wished, MultiQC files of groups that are defined in the sample sheet. By joining this group you can

  1. add existing modules to a pipeline (beginner friendly)
  2. write a new module of your preferred QC tool if it doesn’t exist yet (intermediate level).
  3. start with implementation of long read methods (advanced level, we have only limited experience in the group, so help would be more than appreciated!).
  4. work on display of the data in the MultiQC reports (beginner - intermediate level)
  5. write documentation

Goal: work towards a first release

Group Leaders

Github user FranBonath
Franziska Bonath

Single cell analysis: nf-core/scrnaseq and nf-core/scdownstream

nf-core/scrnaseq transforms FASTQ files into expression matrices, while nf-core/scdownstream receives expression matrices as input and performs quality control, integration, clustering and more. This project has two main parts:

  1. Move some local modules from scdownstream to nf-core/modules so that they can be re-used in scrnaseq.
  2. Add new features to scdownstream. See the open enhancement issues for details.

By joining this group you can:

  1. Create new modules and move existing local modules to nf-core/modules (beginner friendly)
  2. Integrate the newly added modules into the pipelines (beginner - intermediate level)
  3. Improve the scdownstream MultiQC report and documentation (beginner - intermediate level)
  4. Look into a potential extension of scdownstream to multi-omics analyses (advanced level, has not yet been tackled but help would be great!)

Prior experience with single cell analysis is not required, but helpful.

Goal: Move shared functionality to nf-core/modules and make #scdownstream ready for 1.0 release

Group Leaders

Github user nictru
Nico Trummer

Social activities

During the hackathon, we will have light-hearted fun and games! Special prizes are up for grabs for the winners!

More details will be revelealed at the start of the event, but you can expect: a quiz, bingo and sock-related activities.

Helpful resources

Bytesize talks

There are many talks about Nextflow and nf-core on the nf-core Bytesize playlist. In particular, the talk about using git and GitHub in an nf-core environment may be useful.

Tutorials and docs on the nf-core website

Help with coding and nf-core tools

Adding to pipelines

Creating a new pipeline

Code of conduct

Please note that our Code of Conduct applies to the Hackathon, and all participants need to abide by our guidelines to participate. We should all feel responsible for making nf-core events safe and fun for everyone.

You can also report any CoC violations directly to safety@nf-co.re. Our safety officers will contact you to follow up on your report.

In case of an immediate perceived threat at the hackathon, please reach out to any of staff or organizers on site.
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