Channels - the nextflow podcast

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:

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!

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 2024Training at Seqera Sessions — London, 21 March 2024Training 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:

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

Today in the Channels podcast, we're talking about what happened this year in the Nextflow world, with particular emphasis on the many exciting developments in nf-core. We cover: - Community growth (with stats and graphs!) - The evolution of nf-core governance - The latest crop of nf-core pipelines that saw their first release this year and the expansion into domains beyond genomics (even beyond biology!) - Infrastructure updates including subworkflows and testing with nf-test - Community updates including mentorships and training - Upcoming events in 2024: nf-core online hackathon in March, Boston Summit in May and Barcelona Summit in October After today’s episode, we’ll be going on break for the winter holiday and will return in January 2024 with a fun mix of topics. Stay tuned!

In a special edition of the Channels Podcast, Geraldine Van der Auwera interviews four members of the Nextflow community attending the 2023 nf-core hackathon: Raquel Manzano, Edmund Miller, Rieke Hanssen and Francesco Lescai. Recorded in-person at the Nextflow Summit Barcelona, we hear a bit about what they have been working on, how they came to use Nextflow and what motivated them to join the nf-core hackathon.

In a special edition of the Channels Podcast, Phil Ewels chats to Geraldine Van der Auwera! Recorded in-person at the Nextflow Summit Barcelona, we hear a bit about Geraldine’s background - her work at the Broad with GATK and WDL, and the path that brought her to Seqera and the Nextflow community. Oh, and the WDL runner whose name got away is miniWDL, by Mike Lin!

Today in the Channels podcast, we're talking about computing resources... Ben Sherman takes us through new and upcoming runtime improvements in the Nextflow, leading to better performance fine tuning and simpler syntax for pipelines. We cover:

Software containers using Docker / Singularity are a core part of modern data science, found at the heart of Nextflow pipelines. On today's show, we bring on the creator of Nextflow – Paolo Di Tommaso – to tell us the good, the bad and the ugly of containers. He talks about "Wave", one of the newest tools to come out of Seqera Labs and how this can make Nextflow pipelines scale on the cloud, work behind closed doors in protected environments and how it can build & augment images with additional requirements on the fly. And all this whilst reducing the amount of boilerplate code required within your pipeline. As if that wasn't enough, we get a live demo of Wavelit - the open source command-line interface tool, that allows you to leverage the full power of Wave as a stand-alone tool, outside of Nextflow.

In this episode of the Channels podcast, it’s all about developer experience! Ben Sherman takes us through new and upcoming language improvements in the Nextflow language which will help people writing Nextflow pipelines write code faster, with fewer errors, and of course with beautifully formatted indentation 🤩 We cover:

Ever wanted to peer inside Nextflow as it runs your pipeline? We play with an interactive debugger to do just that. Also, a first peek at a new Nextflow Ambassador program, plus a revamped hands-on Nextflow training course.

In this episode of the Channels podcast we have Evan Floden (Seqera Labs CEO) and Harshil Patel (head of scientific development at Seqera Labs) on the show! We talk about: 0:00 - Introduction 1:42 - History of automated testing in nf-core 4:10 - Using Tower CLI with GitHub actions in nf-core 5:09 - Coverage of full-size tests in nf-core 8:00 - Nextflow Tower "pipeline showcase" automation 14:18 - Python library for Tower automation (tw-pywrap) 18:23 - Seqera roadmap: pipeline detail view and run linking 22:06 - Nextflow Tower - Data Explorer 28:01 - Nextflow Tower - Datasets 31:55 - Upcoming events 35:15 - Wrap up

In today's episode of the Channels Podcast, we talk to Seqera software engineer Ben Sherman about what's going on "under the hood" with Nextflow. We touch on task provenance, cloud cache databases and task / sub-workflow grouping. Gotta cache 'em all! 0:00 - Introduction 2:21 - Task provenance 14:32 - Difference to the nf-prov plugin 17:13 - Quilt packages 22:30 - Cloud cache database 32:16 - Task grouping (horizontal) 45:18 - Workflow grouping (vertical) 1:00:22 - Upcoming events 1:03:31 - Close

In this News and Views episode, Chris Hakkaart and Marcel Ribeiro-Dantas talk to Rob Syme about the exciting new Nextflow training material and ways to learn Nextflow in 2023.

In this "News & Views" episode of Channels we talk to Nextflow developer Ben Sherman about some exciting new language features (hopefully) coming soon to Nextflow: 0:00 - Introduction 2:42 - Default values for process inputs 11:59 - Arity, nullable options for input and output paths 28:17 - Named arguments for processes and workflows 36:16 - Map inputs/outputs for processes 41:14 - Custom record inputs/outputs for processes 51:37 - New community content and upcoming events