increasing the default parameter `threads` value

Microbial community profiling WAAFLE
1

Thank you for developing and maintaining WAAFLE! I’ve been using it for my analysis and noticed that the threads parameter significantly affects the runtime. However, the default value seems to be set quite low, which can lead to suboptimal performance on multi-core systems.

I suggest either increasing the default threads value to better utilize available CPU resources or explicitly documenting this parameter in the usage guide so that users can adjust it accordingly. This would help improve efficiency for users who might not be aware of the impact of threads on performance

2

We can definitely adjust the documentation to better advertise the --threads feature. My personal preference is for --threads to default to 1 to avoid overwhelming a user’s system without their knowledge. I find it very frustrating when software defaults to using all available threads! :slight_smile:

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