Today, we’re very happy to announce a new nf-core initiative: Special Interest Groups. These will be a new place to meet and discuss topics with others working in your specific field(s) of research, bringing people together to collaborate in a new way.

Background

nf-core was created to bring people together to collaborate on building Nextflow pipelines. However, as the community grows, the way that we structure ourselves around pipelines and tools is beginning to show a few gaps. Researchers from different disciplines can use the same set of pipelines in very different ways. Most nf-core pipelines are very flexible in their usage by design, and so for truly reproducible research groups need to standardise not just the pipelines that they use, but also the manner in which they use them.

To meet this need, we want to provide a space for community members working on similar research interests to gather and collaborate. We want to foster collaboration not just in the development of scientific research tooling, but also in the usage of that tooling across different fields. We hope that Special Interest Groups will provide a place for this to happen.

How will this work?

The nf-core community is structured around pipelines. The existing methods that we use to manage pipeline groups appears to work well, so rather than reinventing the wheel we intend to adopt a similar pattern for Special Interest Groups:

  1. Anyone can suggest a new group in the #new-interest-group Slack channel
    • Just like with #new-pipelines, there is a Slack workflow with a form to fill in, with a handful of questions to collect all the required information.
  2. The core team (and steering group, as necessary) will discuss the proposal, suggest any changes and either accept or reject the proposal.
  3. A new Slack channel will be created for the new interest group on the nf-core Slack.
  4. A new web page will be created for the group on the nf-core website.
  5. The lead for the new group will organise a nf-core/bytesize talk to introduce the group to the community. A blog post will also be recommended.
  6. The new special interest group will be active and continue under their own steam.

Group web pages

The new web page will just be a stub at first, but we hope that the interest group will develop this over time. These pages can evolve into mini sections with multiple sub-pages, including things like best-practice documentation, meeting notes and more.

The web pages list the nf-core pipelines typically used by members of the group, so that the pages can be cross-linked. That way, anyone viewing a web page for an nf-core pipeline will be able to see at a glance what it can be used for and hopefully link to best practices for that pipeline with that type of data.

Closing after inactivity

Just like pipelines, Special Interest Groups will never be deleted. As part of the annual “spring cleaning” that the nf-core maintainers team does, we will check on each group’s recent activity and make sure that everything is going ok. If a group is obviously inactive and does not respond to requests for a status update, or if desired by the group organisers, the interest group will be archived.

Anyone will be able to revive an archived special interest group at a future date, in a process much like proposing a new group.

Who can join?

Anyone can join any interest group. In the same way that every nf-core pipeline is owned by the community, Special Interest Groups will be made as inclusive as possible.

In order to achieve this, we will try to avoid naming groups after existing groups or consortia, even though some may begin from such origins. We will also try to not to tie any interest groups to very specific topics or research groups where possible. We want anyone working in a relevant field or interest to be able to join an interest group without feeling like an outsider.

What will they do?

We fully expect every interest group to be different: both in their scope and membership, but also in the time that their organisers can commit and the activities that would be most useful to their members. As such, we want to be as flexible as possible with our expectactions. If the group is active and people are finding it useful, we will consider it a success.

That said, the types of things that we hope that interest groups could do could include:

  • Writing best practices for nf-core pipeline usage, specific to their field.
  • Creating pipeline configs specific to the group, to encode these recommendations.
  • Creating and extending nf-core pipelines, as necessary.
  • Working together to harmonise usage of data formats.
  • Listing relevant externala and internal resources, videos and documentation.
  • Holding regular group meetings.
  • Presenting updates in nf-core/bytesize talks and blog posts.
  • Potentially even running their own series of talks, if there is interest.

We’re sure that our new groups can and will do many more different and diverse things. We can’t wait to see where the program goes!

What about pipeline development?

Discussion within Special Interest Groups can revolve around usage of pipelines, but when it comes to any missing features or requirements we expect members to move discussions into the regular pipeline channels. There should be a distinction between scientific and technical topics.

In this way, we hope that interest groups and pipeline groups work in an orthogonal manner, each contributing to the other.

Cross-functional pipelines and interest group structure

Introducing: Our first special interest group

Today we are delighted to announce our first interest group: Animal genomics. We’ll leave the details to be elaborated on in a dedicated blog post by them at a later date, but we’d like to take this opportunity to thank them for taking the lead.

This interest group has formed out of the BovReg and EuroFAANG research consortia. BovReg has been working closely with nf-core since its inception and has helped bring other EuroFAANG consortia members together to use nf-core pipelines, including AQUA-FAANG, EuroFAANG Research Infrastructure, GENE-SWitCH, GEroNIMO, HoloRuminant and Rumigen.

The BovReg project is now reaching its conclusion, and members of the group who had been working closely with nf-core expressed their interest in continuing the collaboration and discussion going in some form. It was this request that led to the formation of nf-core Special Interest Groups. Many thanks to those involved for their enthusiasm and feedback in the process!

Stay tuned for more information about this group, and others. If you have an idea for a group then let us know in the #new-interest-group channel!

Published on
2 April 2024
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