huey VS Apache Kafka

I've considered using Nextflow for bioinformatics pipelines but have yet to take the plunge. At work, I develop a proteomics pipeline that is composed of huey¹ tasks (Python library; simple alternative to Celery) which either use subprocess to call out to some external tool, or are just pure python. It runs in a worker container which is created by docker swarm, and all containers pull jobs from redis. For our scale, it works great. However, I don't have control over the resource utilization of individual steps, and in the past I've had issues with the pipeline blocking as a result of how I was chaining tasks together. I think something like Nextflow would remove these limitations, but one thing I think I would miss is the ability to debug individual pipeline steps locally with an interactive debugger. As far as I can tell, Nextflow has logging/tracing facilities but nothing quite like an interactive debugger. I'd be happy to be told I'm wrong, or even that I'm doing it wrong.

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¹ https://github.com/coleifer/huey/

Other options are DjangoQ and Huey, which tend to work ok. Of the two I prefer DjangoQ. Database backed, don't require the Redis/Celery rigmarole.

Funny, just this moment i finally switched from Celery to huey. And so far I don't regret. huey looks very promising, has good documentation and is well integrated into DJango. You should give it a try: https://github.com/coleifer/huey

huey – a little task queue for python

Huey -> Same again?

Huey: https://github.com/coleifer/huey

I just want to add that a couple celery alternatives worth looking at include huey and dramatiq.

huey

same, I ran into an issue cos of django-background-tasks. I am thinking to replace it with huey

Apache Kafka — a distributed event streaming platform implementing a variant of the Raft consensus protocol (written in Java, integrated with Scala);

Spring does this during autoconfiguration. For example this and this. When the user adds a configuration then it gets to overwrite the default from the template. I am looking for something similar, perhaps simpler approach.

Source and documentation on GitHub

Code is still in trunk though. https://github.com/apache/kafka/tree/trunk/connect/file/src/main/java/org/apache/kafka/connect/file

I briefly described the algorithm in this article and there is a wonderful article from Kafka that goes into more depth in their general purpose implementation. My implementation is specialized and over optimized in comparison, e.g. by using bit manipulation to avoid more expensive division/modulus instructions. Tokio rewrote their timerwheel after I showed them mine, borrowing some ideas but also staying more general. Hope that helps!

Apache Kafka