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
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.