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 Syntax00:07 Welcome and introduction01:20 Language server background04:18 Syntax sugar is just empty calories06:50 Bespoke language syntax08:20 To DSL3 or not 2 DSL10:59 Nextflow versioning15:13 Diving into specifics16:08 Mixing statements with script declarations19:19 Better inspect command21:08 Custom Classes23:32 For loops, while and switch26:02 Standard library26:56 Type annotations28:49 addParams32:26 Process script section34:20 Moving into lib/36:36 Configuration syntax41:14 Relieving pressure from the config43:38 Timelines44:55 The gain for the pain47:54 Next steps48:43 Conclusion
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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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Episode 49: Finding novel proteins at Seanome, with Olga Botvinnik
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
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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
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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