> That's certainly neater. There are many more wrapper that do the same - using 
> mkdtemp() without a dir argument. Is there any plan to perform the same 
> changes on these (bam-to-sam, etc...)?

I made the same change for the BAM to SAM wrapper so that it create temp files 
in the job working directory.

While there is no plan to make these changes across all tools, we'd definitely 
like to see it happen. Making the changes yourself and creating pull requests 
would be a fast, efficient way to get these into the code base.


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