Channels - the nextflow podcast Seqera

Evan Floden (CEO and co-founder of Seqera) joins Phil Ewels (Product Manager for OSS at Seqera) to talk about two of the big announcements at the recent Nextflow Summit Boston 2024 - Seqera Pipelines and Seqera Containers.

We dive into what these two new community offerings are, why we built them and how they work.

Links:


https://seqera.io/pipelines/
https://seqera.io/containers/
Announcement blog post
Nextflow Summit Boston 2024 agenda
Summit YouTube playlist
Nextflow 24.04 blog post



Timeline:

00:00 - Introduction

00:37 - Nextflow Summit Boston 2024

01:14 - Summit talks available online

01:57 - Summit announcements



04:32 - Seqera Pipelines - motivations

05:59 - Seqera Pipelines - first look

06:48 - Testing requirements for community pipelines

10:05 - How we tested pipelines

11:53 - SRA-Explorer tangent



12:34 - Seqera Pipelines - live demo

16:14 - Getting Nextflow launch commands

19:12 - Seqera Containers - intro

24:03 - Seqera Containers - live demo

27:13 - Containers - ARM cpu arch builds

28:33 - Singularity containers

29:09 - Wave CLI

31:19 - Nextflow with Seqera Containers

33:22 - Seqera Containers - future usage



35:09 - Where to read more

36:53 - Thank you to the community

Join us as we discuss the brand new @nf-core / EuroFaang pre-print! 🔥 We chat to some of the key authors, covering the background to the paper, the main messages and how EuroFAANG and nf-core have collaborated. 🧬 👩🏻‍🔬

Join us in this episode of the Channels podcast for a closer look at the Nextflow Ambassadors Program. Marcel Ribeiro-Dantas and Geraldine Van der Auwera discuss the origins of the program, recent highlights and next steps, including the open call for new Ambassadors, which will close June 14.

Relevant links:


Call for applications: https://www.nextflow.io/ambassadors.html
Original announcement: https://www.nextflow.io/blog/2023/introducing-nextflow-ambassador-program.html
Marcel’s favorite Ambassador-contributed Nextflow blog post: https://www.nextflow.io/blog/2024/reflections-on-nextflow-mentorship.html

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.