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.
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-2022channel - 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:
- Follow the link below to find the nf-core hackathon Gather space
- Please note that the hackathon space will not open until October 7
- Enter the email address you used to register for the hackathon
- Check your emails for a one-time code and enter it into the Gather window
- Enter the space and enjoy the hackathon!
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
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.
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:
- 💬 Chat with your group to get an overview of what is going on
- Join the relevant Slack channel to stay up to date and discuss with your project members
- 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
- :raising_hand: 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
- ⏩ When you’re done, make a pull-request with your changes. Link it to the issue so that the issue closes when merged.
- 📄 Describe your work on the HackMD document for the project and tell the group! 🎉
- ♻️ 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 :bow:
Schedule
| Time | Mon. 10 Oct., 2022 | Tue. 11 Oct., 2022 | Wed. 12 Oct., 2022 |
|---|---|---|---|
| 09:00 | Organisers Kickoff | Registration Open | Registration Open |
| 10:00 | Hack! | Quiz! | |
| 11:00 | Registration Open | Hack! | |
| 12:00 | Hackathon arrivals | ||
| 12:30 | Welcome talk | ||
| 13:00 | Lunch | Lunch | Lunch |
| 14:00 | Hack! | Hack! | Wrap-up talk |
| 15:00 | |||
| 16:00 | |||
| 17:00 | |||
| 18:00 | Summary of the day | Summary of the day | |
| 19:00 | Hackathon Social | Hackathon Dinner | |
| 20:00 |
Venue: Torre Glòries
The in-person hackathon will be taking place in Torre Glòries, Barcelona.
Instructions for finding us:
- Use the entrance with the green carpet and a Summit poster
- Find either Lift 7 or Lift 8 (only these lifts!)
- Floor 25
- Turn left and follow the corridor around past the coffee machine
- We are in rooms:
- Eixample (41 people)
- Tibidabo (14 people)
- La Barceloneta (6 people)
- Hack!
| Room name | Door | Inside |
|---|---|---|
| Eixample |  |  |
| Tibidabo |  |  |
| La Barceloneta |  |  |
Video of walking to the hackathon rooms:
Community Streaming Events
Community streaming events are a great way to engage with your local communities while participating in events remotely. By simply booking a room and gathering your colleagues you can create discussion and build your community while enjoying the training, nf-core Hackathon, and/or Nextflow Summit together.
If this is something you are interested in you can tell us about your plans using the link below. We will send you extra material to help you prepare and promote your local event. To get started we have a poster that you can download, edit, and share.
Keep an eye out for others hosting community events in your area. We will be sharing information about community events and how to get in contact with hosts on our website.
You can add your community event using this link.
Social Activities
During the hackathon, we will have a few light-hearted fun and games!
Onsite
- Monday evening: Beers and pizza (non-alcoholic options available) at the Seqera Office!
- Tuesday evening: Dinner!
- The traditional sock hunting in Gathertown will also be held in person! Take pictures of as many socks as you can find.
- Finally, on Wednesday, we will be running a short quiz at 10am with Kahoot!
Online
-
Throughout the three days, we will once again be running a nf-core hackathon bingo! To join the game, you can go the following link. Check the instructions at the bottom of the page.
-
In addition, we will be running a sock hunt once more! There are 11 socks distributed around the gather.town world. Take screenshots of as many as you can find!
-
Finally, on Wednesday, we will be running a short quiz!
All social activities are of course optional, but hope to see as many people joining in as possible 🎉
COVID control
Please remember that the COVID-19 pandemic is not over. If you intend on joining the hackathon in person, we request that you get vaccinated and tested, if possible. We ask for anyone who displays symptoms to not mingle with other participants. Whilst it is not feasible for us to enforce any rules, we request that attendees behave responsibly.
We will be monitoring the status of the pandemic as the event draws closer and reserve the right to make changes in our policies if we deem that to be necessary.
Safety Information at the Hackathon
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.
In addition, please respect the following at all times during the hackathon:
- Do not take screenshots of groups you are working within without asking for consent of all individuals in the group. Remember, not everyone wants their photographs shared on social media.
Reporting CoC Violations during the hackathon
In case of an immediate perceived threat at the hackathon, please reach out to any of the following individuals on Slack. Their names and their location (online/onsite) are indicated.
Safety officers
- Cris Tuñí (onsite)
- Michael Heuer (online)
- Saba Nafees (onsite)
You can also report any CoC violations directly to safety [at] nf-co [dot] re. Our safety officers will contact you to follow up on your report.