Multiple samtools modules use task.cpus-1 without checking for lower boundary
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Description
Have you checked the docs?
Description of the bug
Multiple samtools modules (e.g. depth, index, merge) decrease the task.cpus variable by 1 to set the number of threads. This leads to an invalid setting when using the module for a single core job. I can't see a reason why this is done, as it only makes sense when multiple commands are executed in a pipe, which is not the case here.
Command used and terminal output
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Relevant files
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System information
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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 searching the samtools depth, index, and merge module definitions for task.cpus-1 and compare how each module sets threads. Run the relevant module checks, including the single-core case; done means those modules no longer produce an invalid thread setting for one CPU.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100