Number of cpu is not adapted for fastp tool
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Description
Is your feature request related to a problem? Please describe
Hello,
I notice that the number of cpu for fastp is not adapted. It uses more threads than expected.
Describe the solution you'd like
The --thread option is for worker threads only. Not for all threads used by the tool.
https://github.com/OpenGene/fastp/issues/169:
--thread 2 means use 2 processing worker threads.
Besides the worker threads, fastp uses one master thread, one loader thread, and one or two writer thread (depends on SE or PE).
It should be corrected.
Thank you!
Describe alternatives you've considered
No response
Additional context
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the nf-core module for fastp and inspect how its CPU or process setting is derived. Compare that setting with fastp's documented worker-thread behavior in issue 169; done means the module's configured CPU usage accounts for the additional fastp threads.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 40/100