Introduction

The nf-core hackathon in July this year will be fully virtual, so you can contribute to nf-core and get your pipeline started from the comfort of your homes.

Join us to get help and guidance for writing your own Nextflow pipelines using the best practice guidelines implemented by the nf-core community or contribute to existing pipelines and advancing the current infrastructure. This will be a very informal event and it’s great for learning, sharing ideas and solving issues intensively.

Please note that there are two separate events running in parallel:

  • Nextflow training
    • Mornings - organised through DKFZ
  • nf-core hackathon
    • Register here
    • Afternoons (mornings too if you want) - organised by nf-core community
    • Free to attend!
    • No limit on attendance, everyone welcome

All presentations for both the training and hackathon will be live-streamed to YouTube. The nf-core talks are shown below.

Hackathon registration

Please register to the nf-core hackathon through this google form: https://forms.gle/qo3USZuK2LDJAqHS9

Registration is free and non-binding. This helps us to organise the event: numbers of people, experience and interests allow us to prepare working groups and ensure that presentations are as relevant as possible.

We are hoping to send a few goodies in the post to everyone who registers, so remember to fill in your postal address!

How it works

To participate, all you need is a computer with an internet connection. Presentations will be run using Zoom and live-streamed to YouTube, where they will be also be available afterwards. Discussion and collaboration will be handled in dedicated channels in the nf-core Slack organisation. YouTube streams are embedded in the page below.

For details or questions, please post a message in the #hackathon-july-2020 channel in the nf-core Slack. See https://nf-co.re/join for information on how to join.

All nf-core code is open source with the MIT licence and available on GitHub (https://github.com/nf-core). This event is being organised by the nf-core core team.

Hackathon projects

Work within the hackathon will be loosely gathered into projects. Each project has its own Slack channel and Jitsi meeting room for communication. For the wrap-up daily sessions, the progress made during the day will be presented in the form of HackMD slides.

Tasks, in the form of GitHub issues, can be gathered and organised within the hackathon project board on GitHub: https://github.com/orgs/nf-core/projects/6

If you’d like to form sub-groups, for example to work on a specific pipeline, that’s fine. Just remember to check back in with the main group periodically.

New pipeline development
Existing nf-core pipeline development
Improving nf-core framework tools (written in Python)
Nextflow DSL2 modules

Schedule

The Hackathon will be held on the same dates as a parallel Nextflow workshop

Every day at 13:00 CEST there will be a webinar followed by a Q+A session. After this, a catch-up of the hackathon progress will be held.

The presentations held each day will be as follows:

  • Monday - Introduction to nf-core, tutorial on how to run pipelines
  • Tuesday - Future directions: Nextflow DSL2 and nf-core modules
  • Wednesday - Data management solutions by Elin Kronander
  • Thursday - Tutorial on nf-core tools and guidelines
  • Friday - Feature: nf-core pipelines for common data types & Biocontainers

A remote Pub Quiz will be held on Thursday 17:00-19:00 CEST.

All times are indicated in CEST (Central European Summer Time, UTC+2). If you’re in a different time zone, this time-zone converter tool may be useful.

Monday 13th

Tuesday 14th

Wednesday 15th

Thursday 16th

Friday 17th

Hackathon Introduction

Join the Zoom Meeting for this session.

Welcome talk

Gisela Gabernet (@ggabernet)
Monday 13th, 13:00 - 13:20

Introduction to nf-core

Philip Ewels (@ewels)
Monday 13th, 13:20 - 13:40

An overview of the nf-core community. A little background about how nf-core started and how it has developed over the past three years. I’ll discuss how we communicate and collaborate within nf-core, and cover the nf-core principles and guidelines that we use.

Tutorial: running pipelines

Friederike Hanssen (@FriederikeHanssen)
Monday 13th, 13:40 - 14:00

DSL2 & modules in nf-core

Join the Zoom meeting for this session.

Introduction to DSL2 in Nextflow

Paolo Di Tommaso (@pditommaso) & Evan Floden (@evanfloden)
Tuesday 14th, 13:00 - 13:30

DSL2 in nf-core

Harshil Patel (@drpatelh)
Tuesday 14th, 13:30 - 14:00

Data management solutions

Join the Zoom Meeting for this session.

Elin Kronander (@elinkronander)
Wednesday 15th, 13:00 - 13:30

Click here to download the slides from this talk.

nf-core tools & guidelines

Join the Zoom Meeting for this session.

Philip Ewels (@ewels)
Thursday 16th, 13:00 - 13:30

An overview of the nf-core/tools helper package and how we use this to enforce nf-core guidelines. I’ll describe how template synchronisation works and cover recent changes and improvements so that you know what to expect in upcoming releases.

Virtual social event

_Background picture by Freepik_

Join the Zoom Meeting for the social event. Thursday 16th, 17:00 - 19:00

The virtual social event consists on a Pub Quiz on Nextflow and nf-core followed by a virtual escape room in small teams.

Featured nf-core pipelines & Biocontainers

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nf-core/sarek

Maxime Garcia (@maxulysse)
Friday 17th, 13:00 - 13:20

nf-core/rnaseq

Alex Peltzer (@apeltzer)
Friday 17th, 13:20 - 13:40

nf-core/viralrecon

Harshil Patel (@drpatelh)
Friday 17th, 13:40 - 14:00

Biocontainers

Björn Grüning (@bgruening)
Friday 17th, 14:00 - 14:30

Final wrap-up and closing remarks

Join the Zoom Meeting for this session.

Gisela Gabernet (@ggabernet)
Friday 17th, 16:30 - 17:00
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