Organised by nf-core

Welcome

Please join us for the October 2022 nf-core hackathon!

This hackathon will be held in advance of the Nextflow Summit 2022 in Barcelona, Spain 🇪🇸. You can find out more information about the summit at https://summit.nextflow.io.

In addition to the in-person event, we will endeavour to run a hybrid option online in gather.town.

This hackathon is not meant to be a training event but aimed at people that already have a basic understanding of nextflow and/or nf-core. If you're interested in learning Nextflow and nf-core, there will be free online workshops spanning all global timezones in the week before the hackathon. For more information and the training registration link, see the Nextflow and nf-core training event page.

Registration

Registration for the in-person hackathon event is now closed. You can still register for the on-line event and the Nextflow Summit: https://summit.nextflow.io/register

You can register for either the hackathon or the summit, or both. You're welcome to attend in-person or online. Attendance online is free, attending in person costs €49 (€59 incl. VAT).

• In-person registration is now closed.
• Virtual registration will close October 7, 2022.

Register now

Prerequisites

Prior the hackathon, make sure you're signed up/joined/have installed the following resources necessary for participating in the event:

• Check you agree with the Code of Conduct of the event.
• If you haven’t already, set-up a GitHub account and join the nf-core GitHub organisation.
• Join the nf-core slack and the #hackathon-oct-2022 channel
• Have installed on your computer:
  • Nextflow
  • nf-core/tools
  • Docker/Singularity/Conda: [Google is your friend]
• Familiarise yourself with the documentation on the nf-core website for nf-core modules:
  • https://nf-co.re/docs/contributing/modules
  • https://www.nextflow.io/docs/latest/dsl2.html#modules
  • Relevant nf-core/bytesize talks are also listed below

If you have any problems with any of these just ask on the slack channel or email outreach@nf-co.re

Joining Gather

Only those who have registered will be able to join the hackathon in our Gather space. To join the hackathon in Gather you will need to follow these steps:

1. Follow the link below to find the nf-core hackathon Gather space
   • Please note that the hackathon space will not open until October 7
2. Enter the email address you used to register for the hackathon
3. Check your emails for a one-time code and enter it into the Gather window
4. Enter the space and enjoy the hackathon!

Launch Gather

Interesting Bytesize talks

We have recorded bytesize talks in the past few months going over some of the details of tasks we will be tackling during the hackathon. Take a look if you would like to learn more:

• GitHub contribution basics
• DSL module development
• DSL2 Coding style recommendations (Part 1)
• Updates on the new DSL2 syntax
• Adding modules to nf-core/modules
• How to use modules in a pipeline
• Modules test data
• Test modules
• Where do I start writing my own DSL2 pipeline?!
• Troubleshooting a failed pipeline
• Development environments & workflows (Phil)
• Development environments & workflows (Maxime)
• gitpod.io
• Nextflow Tower CLI

Groups

To keep work and discussion during the hackathon manageable, we will organise everyone into groups. You are free to change groups as you wish during the hackathon.

Since the Nextflow Summit is going to be held just after the hackathon, we decided to keep presentations to a minimum. There will however be some workshops. More details about those will be given closer to the event.

We will coordinate our work and the issues we are working on using a single GitHub project board (we'll post a link to here closer to the time). There will be a separate tab for each group where will have collated a list of relevant issues.

Group 1 - Documentation

This group will focus on all kind of documentation, from pipelines themselves to modules and general documentation to aid in getting started with nf-core and Nextflow. We are also planning on making introduction videos for each pipeline.

#hackathon-oct-2022-documentation

Group leaders

• Abhinav Sharma (in person),
• Marcel Ribeiro-Dantas (in person),
• Franziska Bonath (online)

Group 2 - Subworkflows

Why stop at sharing modules, we want to share subworkflows between pipelines too! Join this group to work on the cutting edge of nf-core development, fleshing out details about how this functionality will work and building proof of concept code to use as a model for the rest of nf-core. Recommended for relatively experienced Nextflow / nf-core contributors only.

#hackathon-oct-2022-subworkflows

Group leaders

• Edmund Miller (in person),
• Harshil Patel (in person),
• Maxime Garcia (in person),
• Yuk Kei Wan (online)

Group 3 - Pipelines

This group will focus on any pipeline related work, this could be:

• DSL2 conversion of a pipeline
• New / improved features for a pipeline
• Entirely new pipelines

#hackathon-oct-2022-pipelines

Group leaders

• Maxime Garcia (in person),
• James Fellows Yates (in person),
• Friederike Hanssen (in person),
• Luis Kuhn (online)

Group 4 - Modules

This group will welcome anyone who wants to work on new modules or improve existing ones.

#hackathon-oct-2022-modules

Group leaders

• Jose Espinosa-Carrasco (in person),
• Gisela Gabernet (in person),
• Louisa Perelo (online)

Group 5 - Infrastructure

The nf-core website is in desperate need of work, and central tooling always needs to be improved and maintained. If this sounds like a fun task, join group 5!

#hackathon-oct-2022-infrastructure

Group leaders

• Matthias Hörtenhuber (in person),
• Júlia Mir Pedrol (in person)

How we will work

We will be a lot of people working in parallel during this hackathon, so to stay organised we have a recommended workflow:

1. Chat with your group to get an overview of what is going on
2. Join the relevant Slack channel to stay up to date and discuss with your project members
3. Find a task to work on using the GitHub Project Board
   • If you have something you want to do that's not there, please make an issue and add it to the board
4. Assign yourself to the issue that you're currently working on (preferably one issue at a time)
   • This is so that multiple people don't accidentally work on the same task
5. When you're done, make a pull-request with your changes. Link it to the issue so that the issue closes when merged.
6. Describe your work on the HackMD document for the project and tell the group!
7. Repeat!

The HackMD document is the easiest to forget, but please add something even if you think what you did was small - we will use it in the group check-outs for each day and also in the reporting after the event so it's important for us

Schedule