Channels - the nextflow podcast Seqera

This podcast episode is quite different to normal. Rather than an interview or a discussion, you'll get to watch as Ben Sherman guides Phil Ewels through the process of creating a new Nextflow Plugin from scratch. Right from the first line of code to creating a release and publishing the plugin.

Nextflow plugins have been getting more attention lately and we've been getting a lot of questions in the community. There is better documentation and resources planned, but in the mean time we hope that this can be a useful guide for anyone curious in how they work, and interested in getting started.

After this we will be back to our usual routine in the podcast, but we'd love to hear what you thought of this taster!




00:00:00 Welcome
00:03:27 Nextflow docs
00:08:34 Starting by forking nf-hello
00:10:32 Overview of project files
00:17:13 Trying a first compile
00:18:12 Different publishing methods
00:19:54 nf-boost local publish method
00:23:05 Trying the new compile
00:24:00 Running locally with the plugin
00:27:32 Looking at the nf-hello plugin code
00:39:29 Deleting files we don't need
00:42:34 Finding event names in the Nextflow source
00:47:46 Writing some custom functions
00:49:41 Testing our new code
00:51:51 Modifying the test pipeline to create files
00:54:14 Coding up the JSON output
00:59:20 Looking at nf-prov code for BCO files
01:05:30 Testing JSON output
01:09:39 Automatic work dir cleanup / nf-boost
01:12:17 Publishing a release on GitHub
01:19:07 Custom plugin repositories
01:26:47 Publishing for all Nextflow users
01:29:52 Conclusion and end

In this episode of Channels, we talk to Jakob Zeitler - Head of R&D at Matterhorn Studios.

We dive into how they use Nextflow and Seqera Platform for material science research, paving the way for cheaper and more eco-friendly products for the future ⚗️👩🏻‍🔬🔬🌎

It may not be bioinformatics, but there's a lot that's in common!

In this episode of the podcast, Geraldine and Ben talk about the Global Alliance for Genomics and Health (GA4GH) and its efforts to develop interoperability standards for pipelining infrastructure.

If the words TES, WES, TRS and DRS are just as much alphabet soup to you, tune in to learn all about how organizations around the world are collaborating to streamline the process of sharing and analyzing data at scale.

In this episode of Channels, we talk to Josh Chorlton - CTO & cofounder of BugSeq Bioinformatics Inc.

We talk about how BugSeq got into using Nextflow and MultiQC and the tips and tricks that they've employed to push scale and performace of their tools to the limit.

We cover topics like testing and CI/CD, passing around structured data objects between Groovy and Python using Protobufs, building Docker images at scale and the ins and outs of using MultiQC for custom clinical data reports.

A recap of our current training formulas, how we got here and where we’re heading to next.



Join us in this episode of the Channels podcast as Geraldine Van der Auwera and Chris Hakkaart discuss options for learning Nextflow in 2024. A recap of our current training formulas, how we got here and where we’re heading to next.



Upcoming training opportunities


Community Foundational Nextflow Training — Online, 5-6 March 2024
Training at Seqera Sessions — London, 21 March 2024
Training at Nextflow Summit — Boston, 21-22 May 2024



Other upcoming events of interest


nf-core Hackathon — Online + Local Hubs, 18-20 March 2024

In this episode of Channels, we talk to Paolo Di Tommaso (creator of Nextflow, Seqera CTO & cofounder) and Jordi Deu Pons (software engineer @ Seqera) about Fusion - a file system written specifically for Nextflow.