The Nextflow Podcast

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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.

3월 16일

Episode 57: Pipeline chaining, meta pipelines and automation (Part 2 of 2)

In episode 57 (March 2026), Phil is joined by Edmund Miller and Ben Sherman to discuss how recent and upcoming Nextflow language changes can make pipeline chaining and meta pipelines easier. The episode was split into two parts: this first part surveyed current solutions, listen to episode 56 to check that out. In this episode we focus on defining workflow “contracts” through clearer inputs (typed params in Nextflow 25.10 and proposed record types, including streamlined sample sheet/record ingestion from CSV/JSON/YAML or queries) and clearer outputs (workflow outputs leaving preview in 25.10, adding an entry-workflow publish section and an output block to publish channels, route files, and serialize channel contents into JSON/CSV/YAML index files). We discuss reducing direct params access inside modules, using records to pass validated param bundles, generating/leveraging nextflow_schema.json for external tooling like Seqera Platform to validate chains, exploring glue pipelines, command-line piping of Nextflow runs, and how lineage IDs could support more data-centric, automated workflows. 00:00 Welcome 01:18 Nextflow language 02:09 Inputs and outputs 04:14 Streamlining sample sheet parsing 07:47 Placement of params 12:03 Sharing workflows 14:09 Outputs 20:04 Workflow ouputs to chain pipelines 25:56 Publishing channels 32:03 Schema 34:37 Schema + pipeline chaining 37:13 Piping pipelines 41:20 Nextflow Lineage 45:56 Conclusion and wrap-up
3월 2일

Episode 56: Pipeline chaining, meta pipelines and automation (Part 1 of 2)

Episode 56 of The Nextflow Podcast (March 2026) focuses on pipeline chaining and meta pipelines in Nextflow, with guests Ben Sherman and Edmund Miller. The episode was split into two parts: this first part surveys current solutions, while part two will cover future Nextflow language changes. The discussion defines meta pipelines as importing pipelines (e.g., nf-core/rnaseq) as subworkflows to form one DAG with parallelization and full resume, versus pipeline chaining using external orchestration to run Pipeline A then feed outputs to Pipeline B. They cover obstacles to meta pipelines in nf-core, including tooling, parameter/config clashes, and tight coupling of pipeline code and configuration. Current chaining approaches include bash/Makefiles, Python, Seqera Platform APIs, nf-cascade (running Nextflow inside Nextflow), wrapping Nextflow with Snakemake, and automation/orchestration tools like Node-RED, n8n, Dagster, and Temporal, including event-driven patterns on AWS. 00:00 Nextflow Podcast, Episode 56 00:08 Welcome 01:42 Introduction to meta pipelines and pipeline chaining 05:01 What makes importing pipelines difficult? 06:55 CLI tooling to import pipelines 09:13 Overlapping config scopes 10:53 Subworkflows or pipelines? 12:38 Pipeline chaining 13:36 nf-cascade 16:42 Nextflow in Snakemake 22:26 Automating Nextflow runs 24:10 Event-driven bioinformatics 26:32 Node-RED + Seqera 30:40 Node-RED flexibility 33:45 Glue code 35:31 Other automation frameworks 37:02 Bioinformatics pipelines vs. ETL workflows 38:56 Tangent: What makes Nextflow special 44:11 Dagster automation demo 47:29 Temporal automation demo 51:13 Wrap up
2월 16일

Episode 55: Terraform & Seqera

In episode 55 of the Nextflow podcast (February 2026), Phil Ewels is joined by Adam Talbot and Ken Brewer to discuss a new Seqera project: using Terraform to manage Seqera Platform configuration as infrastructure as code. They cover why reproducible, reliable infrastructure matters alongside portable Nextflow pipelines, and how Terraform helps reduce “click ops,” provide version control, prevent drift, and support change control via plan/apply workflows and pull requests.The conversation introduces Terraform concepts and highlights use cases such as deploying many workspaces at scale (e.g., universities), regulated clinical environments with approvals, integrating Seqera with existing enterprise Terraform workflows, benchmarking and iterating cloud infrastructure, and managing dev/staging/prod via variables.https://github.com/seqeralabs/terraform-provider-seqera
2월 2일

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
1월 19일

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
2025. 06. 03.

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
2025. 04. 15.

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
2025. 04. 04.

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

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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.

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Seqera
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2021년 - 2026년
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57
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The Nextflow Podcast