Re: [galaxy-dev] samtools BAM to SAM tmp directory

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. Thanks, J.