The Nextflow Podcast

By Seqera

Nextflow is the leading workflow orchestrator for bioinformaticians, data scientists, and professionals in computational biology and genetics. Stay informed with the latest updates, expert interviews,... more

FAQs about The Nextflow Podcast:

How many episodes does The Nextflow Podcast have?

The podcast currently has 59 episodes available.

The Nextflow Podcast episodes:

May 14, 2024 Episode 37: The nf-core / EuroFAANG pre-print
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. 🧬 👩🏻‍🔬
...more
55min
April 30, 2024Episode 36: The Nextflow Ambassadors Program
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
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25min
April 16, 2024Episode 35: Nextflow plugins - A plugin development walkthrough
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
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1h 33min
April 02, 2024 Episode 34: Nextflow in materials science with Jakob Zeitler
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!
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1h 1min
March 19, 2024 Episode 33: GA4GH interoperability standards and Nextflow
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.
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52min
March 05, 2024 Episode 32: Interview with Josh Chorlton
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.

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1h 6min
February 20, 2024Episode 31: Learning Nextflow in 2024
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
...more
29min
February 06, 2024 Episode 30: Fusion file system
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.
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59min
January 23, 2024Episode 29: Nextflow 2023 - 2024
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
...more
1h
January 09, 2024 Episode 28: Seqera and Nextflow in public health — Interview with Kelsey Florek
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
...more
22min

FAQs about The Nextflow Podcast:

How many episodes does The Nextflow Podcast have?

The podcast currently has 59 episodes available.

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The Nextflow Podcast

FAQs about The Nextflow Podcast:

How many episodes does The Nextflow Podcast have?

The Nextflow Podcast episodes:

FAQs about The Nextflow Podcast:

How many episodes does The Nextflow Podcast have?

More shows like The Nextflow Podcast

The Bioinformatics CRO Podcast