New episode alert!
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Episode 56 is all about pipeline chaining and meta pipelines - a topic that’s been on everyone’s mind for years!
I’m joined by @bentsherman and @emiller to explore the various ways people are automating Nextflow, chaining pipelines together, and building meta pipelines today.
The Background:
Anyone else remember when DSL2 was announced in Barcelona in 2019? We all thought meta pipelines would be easy! Seven years later, we’re still figuring it out. This episode dives deep into why it’s been challenging and what people are actually doing about it.
Note: This discussion got so good we split it into two parts! Part 1 covers current solutions, and Part 2 (Episode 57) will cover the future of Nextflow and what’s coming next.
What We Cover:
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Meta pipelines vs. pipeline chaining - what’s the difference?
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Why importing nf-core pipelines as workflows is harder than it looks
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nf-cascade - “Nextflow in Nextflow” by Mahesh Binzer-Panchal
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Nextflow in Snakemake - Edmund’s dark secret revealed!
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Event-driven bioinformatics - automating from sequencer to results
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Node-RED + Seqera - Phil’s low-code automation plugin
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Dagster and Temporal - data engineering tools for pipeline orchestration
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The inevitable “glue code” problem
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What makes Nextflow special for bioinformatics
Pipeline chaining is a natural evolution when running multiple Nextflow pipelines at scale. While there’s no perfect solution yet, the community has created some incredibly creative workarounds - and we’re working on making this better natively in Nextflow!
Show notes, transcript, links and more:
The episode is available now on YouTube, Spotify, and all other podcast platforms! ![]()
As always, the podcast page has a detailed summary plus full transcript. Subtitles are manually curated!
How are you chaining pipelines today? Using any of these tools? Have your own creative solution? Share below - and stay tuned for Part 2!