The Nextflow Podcast

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

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

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

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

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