Introduction

Join us at the first nf-core hackathon for 2021! This event is entirely virtual and we are attempting to support people in all timezones 🌎 🌏 🌍

Registration has now closed, but that doesn’t mean that you can’t join - just jump on Slack and say hi on the #hackathon-march-2021 channel 👋

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 will be embedded in the page below.

For details or questions, please post a message in the #hackathon-march-2021 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. These are not strict and you’re free to work on whatever you would like, they are just to help group together people working on similar tasks.

• DSL2 / modules
  • #hackathon-march-2021-dsl2-modules
  • HackMD
  • Project Board
  • Example tasks: DSL2 pipeline conversion (specific pipelines), writing modules for specific tools, module code linting and tests
• Contribute to a pipeline
  • #hackathon-march-2021-pipelines
  • HackMD
  • Project Board
  • Example tasks: template updates to pipelines, working on specific pipelines (e.g. sarek, scrna)
• Framework tools
  • #hackathon-march-2021-framework
  • HackMD
  • Project Board
  • Example tasks: nf-core/tools, website improvements, input sample-sheet standardisation, RefGenie integration
• Documentation
  • #hackathon-march-2021-documentation
  • HackMD
  • Project Board
  • Example tasks: Make all pipelines use JSON Schema, improving docs about centralised configs, website docs overhaul

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. :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
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 :bow:

Getting help

If you feel lost or stuck, don’t suffer in silence! Hop on to Slack and let us know. You’ll find hackathon mentors there at all hours, marked with a 🧙🏻 in their Slack status. These volunteers are here to help!

Schedule

We expect people to come and go during the hackathon due to diverse time zones. Please just do whatever works best for you and try to catch up with the YouTube streams if you missed them.

• Check-ins and check-outs will be hosted on Zoom and live-streamed to YouTube, available after the event.
• The social will be on Zoom (without YouTube) and Group catch-ups and will be held using https://meet.jit.si/

The following schedule should display times in your local time zone:

Social Activities

During the hackathon, we will have a few light-hearted fun and games.

Throughout the three days, we will 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.

Bingo! https://nfcore-hackathon-2021-03-bingo.web.app/?game=nf-core-hackathon

Furthermore, during Wednesday’s social event (see schedule above), we will be running a short Quiz and escape room!

All social activites are of course optional, but hope to see as many people joining in as possible 🎉

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:

• Never share the jitsi and zoom links for the hackathon on social media.
• 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. Not respecting the latter amounts to doxing, which is also in direct violation of the nf-core Code of Conduct.

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 the time-zones they are located in are indicated.

• Alexander Peltzer (CET)
• Harshil Patel (GMT)
• Phil Ewels (CET)
• Gisela Gabernet (CET)
• James A. Fellows Yates (CET)
• Matthias Hörtenhuber (CET)
• Maxime Garcia (CET)
• Renuka Kudva (CET)
• Kevin Menden (CET)
• Friederike Hanssen (CET)
• Michael Heuer (PST)

You can also report any CoC violations directly to safety [at] nf-co [dot] re. Our safety officer, Renuka Kudva, will contact you to follow up on your report.

In your email report, please do your best to include:

• Your contact information.
• Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct.
• The behaviour that was in violation and the circumstances surrounding the incident.
• The approximate time of the behaviour (if different than the time the report was made)
• Other people involved in the incident if applicable.
• If you believe the incident is ongoing, please let us know.
• If there is a publicly available record (e.g. mailing list record, a screenshot - please attach if so).
• Any additional helpful information.

After you file a report, uur safety officer, Renuka Kudva, will contact you to follow up on your report.

Who will read and handle reports?

All reports will be read and handled by the safety officer at nf-core.

If the safety officer is deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups.

To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with.

Reviewing reports

After receiving the report, the safety officer will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety.

The safety officer in consultation with members of the nf-core core team will assess whether there is sufficient information to determine whether the report constitutes a Code of Conduct violation for them to arrive at a decision on a course of action.

In the case of insufficient information, the safety officer may contact the reporter, the reportee, or any other attendees to obtain more information.

Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any.

The Safety Team reserves the right to not act on a report.

Confidentiality

All reports, and any additional information and data included, are only shared with the safety officer and members of the core team in case the safety officer is in violation of the CoC. We will respect confidentiality requests for the purpose of protecting victims of abuse.

We will not name harassment victims beyond discussions between the safety officer and members of the nf-core team without the explicit consent of the individuals involved.

Enforcement

Actions taken by the nf-core’s safety team may include but are not limited to:

• Asking anyone to stop a behaviour.
• Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently.
• Removing access to the event spaces that we manage either temporarily or permanently.
• Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons.
• Communicating to all participants that an incident has taken place and how we will act or have acted– this may be for the purpose of letting event participants know we are aware and are dealing with the incident.
• Banning anyone from participating in nf-core-managed spaces, future events and activities, either temporarily or permanently.
• No action required.