In this episode of Channels, the Nextflow podcast, join us as we explore Nextflow and AI. Our special guest, Sasha from Seqera, shares his remarkable journey from the consumer tech industry to bioinformatics. Learn about the birth of TinyBio, its innovations in bioinformatics AI applications, and its recent acquisition by Seqera. We delve into AI c…

In episode 44 of the Nextflow Channels podcast, Phil Ewels welcomes Alex Pelzer— a key figure in the Nextflow and nf-core community. Alex shares his journey from academia to the pharmaceutical industry, highlighting the critical role of regulatory frameworks in bioinformatics. 🌟 Key Highlights: The transition from working at QBiC to Boehringer Inge…

In this episode we explore the new features of Seqera's Data Studios and Data Explorer, with Phil Ewels, Rob Newman and Rob Syme from Seqera. Discover how to use these tools for troubleshooting Nextflow pipelines, tertiary analysis and Nextflow development. We discuss the pain points that led to the creation of Data Studios and how it's designed to…

A small but intrepid team of Seqerans recently attended the ISMB 2024 conference in Montreal, a great mix of computational biology and bioinformatics with a largely academic / research-focused audience. Join Geraldine Van der Auwera, Rob Syme and Florian Wuennemann for a lively discussion about the scientific themes of the conference, their experie…

Join us in exploring the latest Nextflow release, 24.04. Phil Ewels and Ben Sherman dive deep into the new updates in Nextflow’s most recent version. We discuss advanced retry strategies, job arrays, resourceLimits, Singularity’s OCI mode, and the game-changing Workflow Output Definition. We’re actively seeking feedback from the community on these …

Join us to hear Phil Ewels chat with Maxime Garciaand Franziska Bonath about how nf-core started at theNational Genomics Infrastructure (NGI) at SciLifeLab in Sweden.We chat about how the nf-core/sarek pipeline grew alongside and eventually joined nf-core,as well as the early days of nf-core bytesize talks and outreach organisation.Links:- SciLifeL…

Tune in to hear all about Pixelgen Technologies - creators of a novel technologyfor doing single-cell spatial proteomics. We chat about how this fascinating technology works, what you can do with the dataand why they chose to develop their analysis suite as an open-source nf-core pipeline. Links: Software: nf-core/pixelator pipeline Pixelator Pytho…

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…

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.next…

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 late…

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…

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 betwee…

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 opportun…

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 …

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…

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 expansi…

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 us…

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 miniWD…

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: Fractional CPU requests resourceLimits directive (to replace check_max) Virtual threads in Groovy WebAssem…

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…

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: What exactly was happening…

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 - Introduction1:42 - History of automated testing in nf-core4:10 - Using Tower CLI with GitHub actions in nf-core5:09 - Coverage of full-size tests in nf-core8:00 - Nextflow …

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 - Introduction2:21 - Task provenance14:32 - Difference to the nf-prov plugin17:13 - Quilt pack…

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 in…

Tune to to Episode 16 of the Channels podcast to hear from the nf-core community infrastructure team: Matthias Hörtenhuber and Júlia Mir Pedrol.In a bumper episode, we discuss the new "nf-validation" Nextflow plugin (https://nextflow-io.github.io/nf-validation/) and talk nf-core components: modules and subworkflows.…

In this News and Views episode, Phil Ewels talks to Ben Sherman about upcoming features in core Nextflow development: a new CLI v2 interface; submission of job arrays and intermediate file cleanup during runs.

In this "News & Views" episode of Channels we kick off the Summer 2023 series of Channels podcasts and go through some of the highlights from the latest Nextflow releases.

A special edition of Channels, Phil Ewels talks to Paolo Di Tommaso and Evan Floden about the past, present and future of Nextflow as the project celebrates its 10th anniversary.

In this "News & Views" episode of Channels we talk about improvements to handling S3 file names, support for the Spack package manager, and local hackathon sites.

In this "News & Views" episode of Channels we talk about the new Sarus container engine, staging outputs using 'rclone' and 'fcp', and using GITHUB_TOKEN to access private repositories.

In this "News & Views" episode of Channels we talk about the new Flux executor for Nextflow, the initiative to add transcripts to all nf-core bytesize videos, and some improvements for error messaging when using Nextflow.

In this "News & Views" episode of Channels we talk about how support for Nextflow DSL1 is going to be dropped and what that means for you. We also explore the wondrous world of AI and ML with a few examples of recent pipelines we've written.

The second "News & Views" episode of Channels - join us as we chat about the nf-test framework for testing Nextflow pipelines, the second round of the Nextflow & nf-core mentorship program and a new Nextflow blog post about how to figure out exactly why your pipeline won't resume!

Rob Lalonde of Seqera Labs interviews Robert Petit, a senior bioinformatics scientist at Wyoming Public Health Laboratory. In this interview, Rob and Rob discuss public health challenges unique to Wyoming, genomic surveillance, the Bactopia pipeline, and the latest fashion trends among leading bioinformaticians in the state.…

The first episode of a new format - meet Channels: the nextflow podcast. We'll be joining Rob Lalonde in bringing podcast episodes to your feeds with short News & Views episodes where you can hear us discuss hot topics in the Nextflow community.

In this Podcast, Rob Lalonde of Seqera Labs speaks with Dr. Evan Floden, CEO and co-founder of Seqera Labs. Rob and Evan talk about the history of Nextflow, breaking bad, and the future of bioinformatics. Evan also provides a live demo of Nextflow Tower.

In this Podcast, Rob Lalonde of Seqera Labs speaks with Cedric Notredame, head of the Notredame Lab at the Centre for Genomic Regulation in Barcelona, Spain. In this far-ranging discussion, Rob and Cedric talk about cloud, pipelines, and trace the evolution of Nextflow from its early days as a research project to its current role in the global COVI…

In this Podcast, Rob Lalonde of Seqera Labs speaks with Lorena Pantano, head of Computational Biology at NextRNA, a firm leading the next revolution in RNA-directed therapeutics located in Cambridge, Massachusetts. In this fascinating discussion, Rob and Lorena talk Bioinformatics, life in a startup, and women in technology.…

In this Podcast, Rob Lalonde speaks with Nils Homer, founding partner at Fulcrum Genomics. Nils shares his unique perspectives on breaking into the bioinformatics industry, advances in technology and tools, and what to expect in the next three to five years.

In this Podcast, Rob Lalonde speaks with Phil Ewels of SciLifeLab Sweden, part of NGI Stockholm. In this fascinating discussion, they cover everything from nf-core to future bioinformatics challenges.