common-workflow-
huey
| common-workflow- | huey | |
|---|---|---|
| 1 | 10 | |
| - | 4,927 | |
| - | - | |
| - | 6.2 | |
| - | 6 days ago | |
| Python | ||
| - | MIT License |
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common-workflow-
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Nextflow: Data-Driven Computational Pipelines
https://www.commonwl.org/
https://github.com/common-workflow-language/common-workflow-...
huey
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Nextflow: Data-Driven Computational Pipelines
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/
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Background jobs with Django
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.
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What's the best thing you've learned about Django this year?
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
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This Week in Python
huey – a little task queue for python
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What is your favourite task queuing framework?
Huey -> Same again?
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5 background scheduling libraries in Python you must know
Huey: https://github.com/coleifer/huey
- Celery in production: Three more years of fixing bugs
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Not sure if I should use celery or asyncio
I just want to add that a couple celery alternatives worth looking at include huey and dramatiq.
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What is the best option for a (Python 3) task queue on Windows now that Celery 4 has dropped Windows support?
huey
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Django 4.0 released
same, I ran into an issue cos of django-background-tasks. I am thinking to replace it with huey
What are some alternatives?
redun - Yet another redundant workflow engine
celery - Distributed Task Queue (development branch)
common-workflow-language - Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊
rq - Simple job queues for Python
cgpipe - cgpipe - minimum viable HPC pipeline
dramatiq - A fast and reliable background task processing library for Python 3.
nextflow - A DSL for data-driven computational pipelines
RabbitMQ - Open source RabbitMQ: core server and tier 1 (built-in) plugins
mrq - Mr. Queue - A distributed worker task queue in Python using Redis & gevent
KQ - Kafka-based Job Queue for Python
django-background-tasks - A database-backed work queue for Django
Streamz - Real-time stream processing for python