Episode 33: GA4GH interoperability standards and Nextflow

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.

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.

Join us in this episode of the Channels podcast to get a recap of some of the biggest features to be added to Nextflow in 2023 and take a look at some of the things coming in 2024. We tried to do this in Episode 27 but ended up spending nearly all the time discussing community and nf-core, so this episode is dedicated to just Nextflow features. We cover Phil's top hits: 2023 Fusion support on Azure Batch, Google Batch, SLURM, LSF Spack integration Markdown docs, developer docs New `nextflow inspect` command Channel "topics" AWS Fargate for compute tasks 2024 Job arrays Garbage collection (aka work directory cleanup) Command line interface v2 Improvements to Nextflow packaging Workflow inputs and outputs schema Module configuration / config v2

Rob Lalonde of Seqera interviews Kelsey Florek, Senior Genomics and Data Scientist at the Wisconsin State Laboratory of Hygiene. In this interview, Rob and Kelsey discuss how genomic surveillance has changed since the COVID pandemic, and how Seqera Platform and Nextflow pipelines have substantially lowered the barrier to entry for bioinformaticians running workflows in public health labs and in the field. The viralrecon pipeline Kelsey mentioned in the interview can be found at https://nf-co.re/viralrecon