The Nextflow Podcast
by Seqera

In this episode, Phil Ewels speaks with Dr. Olga Botvinnik, founder and CEO of Seanome, who shares her journey from computational biology to marine genomics.

In this episode of the Nextflow Podcast, we dive into highlights from the recent Nextflow Summit held in Barcelona in 2024. The summit featured an incredible range of talks, demonstrations, and discussions showcasing the latest advancements in workflows, data analysis, and community collaboration.

In this episode, Phil Ewels and Ben Sherman discuss the launch of the new Nextflow language server, a significant upgrade providing advanced code intelligence features such as code completion and error hints for VS Code users.

Join Geraldine Van der Auwera and Ben Sherman as they dive into the differences and similarities between Nextflow and the Workflow Description Language (WDL). They discuss the origins and development of WDL at the Broad Institute, the challenges of working with different workflow languages, and how Nextflow’s channel-based data flow model compares to WDL’s approach.

In episode 45 of the Channels podcast, Sasha Dagayev from Seqera (formerly tinybio) shares his journey from working in tech and consumer spaces to entering bioinformatics during the pandemic. Sasha discusses the challenges and innovations behind tinybio, including the evolution towards integrating Generative AI (ChatGPT) to simplify bioinformatics tasks.

Phil Ewels talks with Alex Pelzer about the importance of regulatory compliance for bioinformatics and Nextflow pipelines. We discuss how documentation, software testing, and standardization all plays a part in ensuring pipeline reliability for clinical trials. We also chat about the new nf-core Regulatory Special Interest Group, aiming to collaborate on best practices and standards for bioinformatics pipelines.

In this episode Phil Ewels hosts Rob Newman and Rob Syme to explore Data Explorer and Data Studios. These can revolutionise bioinformatics development, with tterative Nextflow development reducing friction with cloud computing and speeding up both pipeline scripting and tertiary analysis.

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 experience running a booth, meeting with the ISMB and BOSC community, and resources for job seekers.

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 new "topics", "eval", advanced retry strategies, job arrays, resourceLimits, Singularity’s OCI mode, and the game-changing Workflow Output Definition.

Join us to hear Phil Ewels chat with Maxime Garcia and Franziska Bonath about how nf-core started at the National 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.

Meet nf-core/pixelator - the Molecular Pixelation pipeline Tune in to hear all about Pixelgen Technologies - creators of a novel technology for doing single-cell spatial proteomics.

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.

Join Phil Ewels, Cedric Notredame, Jose Espinosa-Carrasco and Friederike Hanssen as they discuss the brand new pre-print describing updates to the nf-core community and framework together with the experience of the EuroFAANG consortia as they integrated with nf-core.

A closer look at the Nextflow Ambassadors, a worldwide initiative designed to foster collaboration, knowledge sharing, and community growth. It is intended to recognize and support the efforts of our community leaders and marks another step forward in our mission to advance scientific research and empower researchers. Marcel and Geraldine discuss the origins of the program, recent highlights and next steps.

Ever wondered about how Nextflow plugins work? Join us for this walk through tutorial, as Ben Sherman guides Phil Ewels to create and publish a plugin from scratch. Right from the first line of code to creating a release and publishing the plugin.

We speak to Jakob from Matterhorn Studio about how they use Nextflow and Seqera Platform in materials science research.

In this episode of the podcast, Geraldine Van der Auwera and Ben Sherman talk about the Global Alliance for Genomics and Health (GA4GH) and its efforts to develop interoperability standards for pipelining infrastructure.

In this episode of Channels, Phil Ewels talks to Josh Chorlton - CTO & cofounder of BugSeq Bioinformatics Inc. We talk about infrastructure and backend for Nextflow and MultiQC in clinical practice.

Join Geraldine Van der Auwera and Chris Hakkaart discussing options for learning Nextflow in 2024. A recap of our current training formulas, how we got here and where we’re heading to next.

Super-fast data access for Nextflow pipelines. In this episode of Channels, Phil Ewels talks 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 as Geraldine Van der Auwera and Phil Ewels 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.

Rob Lalonde interviews Kelsey Florek about using Nextflow, nf-core pipelines and Seqera platform for genomic surveillance in public health labs.

In this Community Highlights episode, Phil Ewels and Geraldine Van der Auwera discuss what happened this year in the Nextflow world, with particular emphasis on the many exciting developments in nf-core.

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.

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.

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 gives us the rundown on Wave containers. We talk about how wave makes pipelines faster and more secure, all with simpler & cleaner code!

In this episode of the Channels podcast, it’s all about developer experience! We chat about debugging, error messages and language servers.

Ever wanted to peer inside Nextflow as it runs your pipeline? We play with an interactive debugger to do just that. We also give a first look at plans for a brand new “Nextflow Ambassador” program that we’ll be launching soon, as well as a revamped training course that was rescued from the precipice.

In this News and Views episode, Phil Ewels talks to Evan Floden and Harshil Patel from Seqera about automation of pipeline testing, Nextflow Tower CLI and automation. We wrap up with a sneak-preview of some future road map items coming soon to Nextflow Tower.

In this News and Views episode, Phil Ewels and Chris Hakkaart 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!

Chris Hakkaart and Marcel Ribeiro-Dantas talk to Rob Syme about the exciting new Nextflow training material and ways to learn Nextflow in 2023.

Ben Sherman tells us about future improvements to Nextflow syntax for processes.

Join us as we discuss the new nf-validation Nextflow plugin and talk nf-core components: modules and subworkflows.

We talk to Nextflow developer Ben Sherman about some exciting new features coming soon to Nextflow: a new CLI v2 interface; submission of job arrays and intermediate file cleanup during runs.

Welcome back to the Summer 2023 series of the Channels Podcast! In this episode we kick things off with some of the highlights from the latest Nextflow releases. There were a lot of goodies in there..

Phil Ewels, Paolo Di Tommaso and Evan Floden look back on 10 years of scientific workflows.

S3 file names, Spack package manager support and local hackathon sites.

The Sarus container engine, staging outputs and the GITHUB_TOKEN.

The Flux executor, bytesize transcripts and improved error messaging.

Updates to the Nextflow language and putting ML pipelines to good use..

nf-test, mentorships and debugging resume

Pathogens, Bactopia and awesome shirts. Rob Lalonde of Seqera 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.

An introduction to the News and Views episode format.

In this Podcast, Rob Lalonde of Seqera speaks with Dr. Evan Floden, CEO and co-founder of Seqera. 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 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 COVID effort.

Inside a Bioinformatics Startup – with NextRNA Therapeutics.

Seqera speaks to Nils Homer of Fulcrum Genomics about the bioinformatics industry, advances in technology and tools, and coming industry developments.

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.