In this episode of Channels, the Nextflow podcast, host Geraldine Van der Auwera from Seqera and her colleague Ben Sherman 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. The conversation covers key features, type systems, and runtime specifications, highlighting the strengths and limitations of both languages. Ben hints at upcoming improvements and enhancements for Nextflow, aimed at making the language more robust and user-friendly. The episode offers valuable insights for bioinformaticians and developers navigating the complexities of workflow management.
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. <!-- end-archive-description --> We discuss:
In episode 44 of the Channels podcast, Phil Ewels Phil talks with Alex Pelzer, a key figure in the Nextflow and nf-core communities, about regulatory aspects of bioinformatics and Nextflow pipelines. We talk about Alex’s background, his experience in academia(QBiC) and industry (Boehringer Ingelheim), and the importance of regulatory compliance in bioinformatics workflows. We discuss how documentation, software testing, and standardization all plays a part in ensuring pipeline reliability for clinical trials. Finally, we highlight the newly formed 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, reducing friction with cloud computing and speeding up both pipeline scripting and tertiary analysis. We talk about:
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 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.
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.
Join us in this episode of the Channels podcast for 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 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.
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.
In this episode of Channels, we talk to Jakob Zeitler - Head of R&D at Matterhorn Studios.
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.
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.
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.
In this episode, Rob Lalonde of Seqera interviews Kelsey Florek, Senior Genomics and Data Scientist at the Wisconsin State Laboratory of Hygiene.
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 – to tell us the good, the bad and the ugly of containers.
In this episode of the Channels podcast, it’s all about developer experience! 👩🏻💻🎉
In this News and Views episode, Phil Ewels, Chris Hakkaart and Marcel Ribeiro-Dantas play with interactive debuggers in IntelliJ to try to understand what’s happening in their pipeline. 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!
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 and Views episode, Phil Ewels and Marcel Ribeiro-Dantas talk to Ben Sherman about the exciting work in progress related to the Nextflow language.
In this News and Views episode, Phil Ewels and Chris Hakkaart talk to Júlia Mir Pedrol and Matthias Hörtenhuber - the nf-core infrastructure team.
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 and Views episode, Phil Ewels, Chris Hakkaart and Marcel Ribeiro-Dantas discuss the hottest topics in the Nextflow world.
Today marks 10 years since Paolo Di Tommaso made the first commit for Nextflow!
In this News and Views episode, Chris Hakkaart and Marcel Ribeiro-Dantas discuss the hottest topics in the Nextflow world.
In this News and Views episode, Chris Hakkaart and Marcel Ribeiro-Dantas discuss the hottest topics in the Nextflow world.
In this News and Views episode, Chris Hakkaart and Marcel Ribeiro-Dantas discuss the hottest topics in the Nextflow world.
In this News and Views episode, Phil Ewels, Chris Hakkaart, and Marcel Ribeiro-Dantas discuss the hottest topics in the Nextflow world.
In this News and Views episode, Phil Ewels, Chris Hakkaart, and Marcel Ribeiro-Dantas discuss the hottest topics in the Nextflow world.
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.
In this News and Views episode, Phil Ewels, Chris Hakkaart, and Marcel Ribeiro-Dantas discuss the hottest topics in the Nextflow world.
In this Podcast, Rob Lalonde, CCO of Seqera speaks with Dr. Evan Floden, CEO and co-founder of Seqera. Rob and Evan talk about the history of Nextflow, Evan’s journey as the co-founder of a start-up, 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.
In this podcast, Rob Lalonde of Seqera 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.
