The Nextflow Podcast

Seqera

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LIFE SCIENCES

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, and insights from the Nextflow ecosystem with The Nextflow Podcast, by Seqera. Follow us on Twitter @nextflowio and YouTube @Nextflow.

5D AGO

Episode 54: Fusion Snapshots, with Lorenzo Fontana

In this episode, Phil Ewels sits down with Lorenzo Fontana, an engineer at Seqera with deep expertise in Linux kernel internals, eBPF, and systems programming. Full transcript and summary blog post here: https://seqera.io/podcasts/episode-54-fusion-snapshots/ Lorenzo is the co-author of the O'Reilly book "Linux Observability with eBPF" and a key developer behind Fusion and Fusion Snapshots. We explore Lorenzo's fascinating journey from Linux security tools to bioinformatics infrastructure, and take a technical deep dive into how Fusion Snapshots actually work under the hood: including CRIU, incremental dumps, and how tasks can be frozen and migrated between cloud instances in under two minutes.🔗 Links mentioned in this episode:Fusion & Seqera:• Fusion Snapshots Blog Post: https://seqera.io/blog/fusion-snapshotting/• Try Fusion Snapshots with Seqera Compute: https://seqera.io/platform/Lorenzo's Background:• Linux Observability with BPF (O'Reilly): https://www.oreilly.com/library/view/linux-observability-with/9781492050193/• Falco Runtime Security: https://falco.org/Open Source Projects:• criu-static: https://github.com/seqeralabs/criu-static• staticreg: https://github.com/seqeralabs/staticreg• CRIU Project: https://criu.org/⏱️ Timestamps:00:00 Nextflow Podcast ep54: Lorenzo Fontana00:04 Welcome and intro01:33 Background in eBPF06:46 Becoming an expert in eBPF11:29 O'Reilly Book13:02 Falco and linux kernel bugs16:07 Move to Seqera20:42 Intro to Fusion26:18 Comparing Fusion to other solutions29:00 Fusion Snapshots31:15 How Fusion Snapshots moves tasks35:58 Contributions back to CRIU39:05 criu-static43:12 staticreg44:36 Fusion Snapshots broken down46:50 Fusion Snapshot spot reclamation50:18 Incremental dumps53:59 Fusion snapshot process timing57:25 Seqera full stack59:20 Call to action01:00:52 pigz01:03:41 How to try Fusion Snapshots01:04:42 AI usage in the future01:11:06 Wrap up📢 Connect with us:• Community forum: https://community.seqera.io• nf-core: https://nf-co.re• Seqera: https://seqera.io#Nextflow #Bioinformatics #CloudComputing #Seqera #FusionSnapshots #SpotInstances #eBPF #Linux

1h 13m
JAN 19

Episode 53: Highlights from 2025

The Nextflow Podcast is back! After a brief hiatus, Phil Ewels returns with a comprehensive look at everything that happened in 2025 across the Nextflow ecosystem. Joining Phil for this year-in-review are Rob Syme (Scientific Support Lead), Marcel Ribeiro Dantas (Senior Developer Advocate), and Rob Newman (Product Manager Lead) from Seqera.In this episode, we cover:* Nextflow Language Evolution - The new syntax parser, VSCode extension with native language server support, nextflow lint and format commands, and the game-changing Lineage tracking feature for full data provenance. * Plugin Ecosystem - The new plugin registry at registry.nextflow.io, easier plugin development, and the complete AWS SDK v2 rewrite for dramatically improved S3 performance at scale.* Workflow Inputs and Outputs - How workflow outputs are replacing publishDir, typed parameters, and the foundations being laid for static types in Nextflow.* Seqera Platform Updates - The redesigned pipeline run details page, single-VM compute environments with 4-6x faster startup, Seqera Compute, Fusion Snapshots for spot instance resilience, Studios improvements, and Data Explorer S3 API support.* AI and Automation - Seqera AI developments, the MCP server for integrating with Claude/Cursor/Copilot, and Node-RED integration for pipeline chaining and automation.* Community Growth - nf-core tools releases, the syntax adoption roadmap, Nextflow Summits in Boston and Barcelona, the Ambassador program expanding to 40 countries, Training Weeks, and Seqera's Series B funding.Links mentioned in this episode:- Nextflow Plugin Registry: https://registry.nextflow.io- Node-RED Integration: https://seqera.io/blog/node-red/- Seqera MCP Server: https://seqera.io/blog/seqera-mcp/- nf-core Syntax Roadmap: https://nf-co.re/blog/2025/nextflow_syntax_nf-core_roadmap- Fusion Snapshots: https://seqera.io/blog/fusion-snapshotting/- Seqera Compute: https://seqera.io/blog/seqera-compute-public-preview/Subscribe to stay updated on all things Nextflow, and check out the full show notes at seqera.io/podcast00:00 Nextflow Podcast - Episode 53: 2025 Recap00:09 Welcome01:10 Introductions02:54 Nextflow Language Evolution03:44 Nextflow VSCode Extension06:47 Nextflow lint and format08:21 Nextflow Lineage12:33 Nextflow Plugin Registry17:29 AWS SDK v2 upgrade21:09 Workflow Inputs/Outputs and Static Types26:38 Seqera Platform: Pipeline Run Details29:57 Dynamic resource labels30:56 Pipeline versioning31:58 Pipeline Chaining with Node-RED35:07 Single VM Compute Environments39:14 Seqera Compute41:24 Fusion Snapshots44:32 Seqera AI49:03 Seqera MCP Server50:04 Data Explorer & s3 APIs51:24 Datasets52:54 Seqera Studios Updates56:56 Seqera company updates57:31 nf-core/tools updates58:41 Topics01:00:05 Syntax updates in nf-core01:00:55 Community growth01:03:43 Nextflow Summits and events01:05:00 Nextflow Ambassadors01:07:19 Training Weeks01:09:13 Wrap up

1h 12m
06/03/2025

Episode 52: Australian BioCommons

In Episode 52 of the Nextflow podcast, Phil Ewels is joined by Ziad Al Bkhetan and Steven Manos from the Australian BioCommons to explore how Nextflow and Seqera Platform are transforming bioinformatics research across Australia. Discover how the Australian BioCommons emerged as a national infrastructure investment to support molecular life sciences researchers, building digital platforms and tools that serve diverse research communities - from genome assembly to proteomics. Learn about their journey from identifying Nextflow as the leading workflow management system in Australia to successfully deploying Seqera Platform for over 90 users across 18+ research institutions. The conversation covers fascinating success stories including the collaborative development of the nf-core/proteinfold pipeline, supporting structural biology researchers with advanced protein folding tools, and the innovative Ozark community phylogenetic trees workflow. Steven and Ziad share insights on overcoming challenges like integrating web platforms with traditional HPC infrastructure at Australia's tier-one supercomputing facilities (NCI and Pawsey), and building hybrid compute environments that seamlessly span local HPC and cloud resources. Key highlights include Australia's growing contribution to the global nf-core community, culminating in their first official participation in the March 2025 nf-core hackathon with a dedicated Sydney hub. The team also discusses practical advice for other countries looking to establish national Nextflow services, emphasizing the importance of building local expertise and community engagement. For Australian researchers interested in accessing these services, visit biocommons.org.au to learn more about available platforms, training opportunities, and community resources. 00:00 Podcast Ep 52: BioCommons 00:06 Welcome 00:41 Ziad - introduction 01:36 Steven - introduction 03:40 Introduction to Australian BioCommons 08:13 Nextflow usage in Australia 09:05 BioCommons collaboration with Seqera 12:24 Compute infrastructures in Australia 15:05 Nextflow support & training 16:43 Highlights and lowlights 19:11 Protein fold 21:50 Ozard Community 23:39 Automation with Seqera Platform 25:52 Nextflow Communty in Australia 29:27 2025 nf-core hackathon 31:57 Future plans for Nextflow & Seqera Platform 33:04 Tips for building a National Nextflow platform 36:21 Next steps 37:51 Wrap up Resources: Australian BioCommons: https://biocommons.org.aunf-core office hours: https://nf-co.re/blog/2025/apac-helpdesk-2025

39 min
04/15/2025

Episode 51: Nextflow strict syntax

In Episode 51 of the Nextflow podcast, Phil Ewels and Ben Sherman discuss Nextflow's upcoming strict syntax - a significant evolution bringing clearer error messages and a more consistent language framework. They explore key changes including the separation of code from declarations, removal of for/while loops in favour of operators, and changes to type annotations. Learn how these improvements lay the groundwork for better developer experiences with features like static type checking and auto-formatting. The episode covers migration timelines, practical steps to prepare, and how these changes will ultimately lead to more robust, maintainable pipeline code. Check out the Nextflow docs for the "Updating Nextflow Syntax" guide to start preparing today. 00:00 Podcast Ep51: Strict Syntax 00:07 Welcome and introduction 01:20 Language server background 04:18 Syntax sugar is just empty calories 06:50 Bespoke language syntax 08:20 To DSL3 or not 2 DSL 10:59 Nextflow versioning 15:13 Diving into specifics 16:08 Mixing statements with script declarations 19:19 Better inspect command 21:08 Custom Classes 23:32 For loops, while and switch 26:02 Standard library 26:56 Type annotations 28:49 addParams 32:26 Process script section 34:20 Moving into lib/ 36:36 Configuration syntax 41:14 Relieving pressure from the config 43:38 Timelines 44:55 The gain for the pain 47:54 Next steps 48:43 Conclusion

50 min
04/04/2025

Episode 50: Imaging pipelines and analysis, with Krešimir Beštak

In this milestone 50th episode of the Nextflow podcast, host Phil Ewels sits down with Krešimir Beštak, a PhD student and active contributor to the nf-core community, to explore an exciting frontier in bioinformatics: microscopy and spatial omics. While Nextflow is traditionally associated with genomics workflows, Krešimir shares how it’s being used to power image analysis pipelines like MCMICRO, supporting complex research into cardiovascular disease and cancer diagnostics. Based at the University Hospital Heidelberg, Krešimir discusses his transition from master’s student to PhD researcher, the translational applications of spatial proteomics, and how Nextflow enables reproducible workflows far beyond its original scope. 00:00 Podcast Ep 50: Krešimir00:09 Welcome and introductions03:13 Introduction to Spatial Omics04:26 Multiplexing markers06:38 Metabolite microscopy07:23 Myocardial multiomics08:58 Microscopy data analysis11:32 nf-core/mcmicro13:05 2D vs 3D microscopy13:38 Computational bottlenecks within analysis15:43 Other nf-core imaging pipelines18:36 Downstream analysis after molkart19:53 Manual interventions23:27 Minerva25:39 Google Maps for cells27:16 Microscopy community around Nextflow30:34 How to get involved31:38 Changes in Nextflow for microscopy32:43 Nextflow Ambassador program33:17 Conclusion

35 min
03/18/2025

Episode 49: Finding novel proteins at Seanome, with Olga Botvinnik

Join host Phil Ewels in Episode 49 of the Nextflow Podcast as he interviews Dr. Olga Botvinnik, founder and CEO of Seanome. Olga discusses her journey from studying at MIT to founding her non-profit research institute focused on marine genomics. Discover her groundbreaking work in annotating unknown proteins and her efforts in collaborating with the Earth BioGenome Project. Olga also shares her experience with the Nextflow and nf-core communities, and her vision for developing tools to aid research in understudied ocean organisms. Join us as we chat about the vast potential of marine genomics and its applications. 00:00 Podcast Episode 49: Olga Botvinnik / Seanome 00:06 Welcome 01:18 Olga's background 07:30 Colonial tunicates 09:38 Starting Seanome with Arctic clams 11:07 Vision for Seanome 12:46 Earth BioGenome Project 13:46 Animal genomics not metagenomics 14:53 Building nf-core/proteinannotator 19:46 Software engineering in bioinformatics 22:21 nf-core early days 27:46 Bioinformatics Beyoncé 30:50 Seanome future steps 32:10 Final thoughts: Why the ocean 34:19 Goodbyes

35 min
11/28/2024

Episode 48: Nextflow Summit Barcelona 2024 Highlights

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. With so much exciting content to explore, we’ve picked out some of our favourite moments to share with you. From impactful new features to inspiring keynote addresses and humorous presentations, this episode offers a curated selection of clips that capture the energy and innovation from the event. Join us as we relive the summit’s best bits and discuss their significance for the Nextflow community. 00:00 Start 00:10 Podcast introduction 00:47 Introductions: Group 1 01:56 Clip 1: Wave mirroring 04:32 Clip 2: Throwing cat food 06:00 Clip 3: crisprseq 08:03 Clip 4: nf-test 10:34 Clip 5: Workflow output definition 12:39 Clip 6: Open Science Software Foundation launch 15:08 Clip 7: FAIR code with nf-core 16:58 Clip 8: Teaching with Nextflow 18:56 Clip 9: Conda lock files 21:24 Clip 10: MultiQC in scripts 22:43 Clip 11: Small Nextflow Big Nextflow 25:17 Introduction: Team 2 26:11 Clip 12: Genomics England 29:47 Clip 13: Alphafold interactive reports 33:26 Clip 14: Data Studios 35:32 Clip 15: Covid and Ebola 37:35 Clip 16: Seqera AI 41:34 Clip 17: Nextflow VSCode DAGs 44:33 Clip 18: Fusion snapshots 48:38 Clip 19: Sustainable computing 52:38 Clip 20: nf-core/tools 56:37 Clip 21: Industry best practices with nf-core 58:58 Clip 22: Federated data queries 01:01:56 Clip 23: Nextflow Ambassadors 01:05:04 Conclusion

1h 6m
11/05/2024

Episode 47: New Nextflow language server & VS Code extension

In episode 47 of The Nextflow Podcast, 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. They detail the benefits of formalizing Nextflow as its own programming language, reducing reliance on Groovy, and improving error messages and code clarity. They also cover new documentation, plans for future features like type annotations, and encourage community feedback and adoption. Find the new docs here: https://www.nextflow.io/docs/latest/vscode.html 00:00 Podcast Ep 47 - Version 2 - VSCode Extension 00:09 Welcome and introductions 00:44 Podcast rebranding 01:29 Nextflow Summit announcements 02:48 Language server background 06:27 Nextflow as a programming language 09:58 Building a language server 14:12 VS Code interactions with the language server 15:22 VS Code demo 15:50 Errors + warnings tray 17:10 Errors: Level 0 20:00 Errors: Level 1 22:32 Errors: Level 2 23:02 To def or not to def 24:46 Variable references 25:34 Number of arguments 25:57 Hover hints on workflows and processes 26:19 Code navigation 26:52 Output hints 27:17 Code peeks 27:56 Getting help 28:29 Code formatting 30:25 Nextflow schema params 32:03 Future warnings 34:02 Preview DAG 34:54 Fixing new syntax errors 35:42 Config files 37:07 Updating the plugin 37:33 Roadmap: Type checking 38:55 Conclusion

40 min

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, and insights from the Nextflow ecosystem with The Nextflow Podcast, by Seqera. Follow us on Twitter @nextflowio and YouTube @Nextflow.

Creator

Seqera
Years Active

2021 - 2026
Episodes

54
Rating

Clean
Copyright

© Seqera
Show Website

The Nextflow Podcast