Nextflow: Data-Driven Computational Pipelines

Re:Nextflow: Data-Driven Computational Pipelines by jromma on Friday August 11, 2023 @12:08AM (#37085012)

I'm personally a huge fan of redun¹ for running computational pipelines. It's pure python, it's easy to learn/debug, it has automatic caching, retry, provenance logging, and a great integration with AWS Batch for running large jobs. I've been really impressed with how easy it is to run a job to completion that fans out to thousands of AWS spot instances at once.

I've used nextflow in the past, and I've found it to be much harder to use. Learning another DSL is annoying, documentation was sparse, I constantly ran into bugs, and it was hard to debug in general. I don't know how much it's changed over the past 3 years though.

¹https://github.com/insitro/redun

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Re:Nextflow: Data-Driven Computational Pipelines by radus on Friday August 11, 2023 @01:08PM (#37091063)

This is the first time I've seen this and it looks very interesting -- thank you for sharing!

I described my workflow in a different comment on this post, and this seems like something I could port to with minimal changes in code since every step is already a Python function and even decorated by @task.

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