MarkDuplicates Queue extension and intermediate files
I was frustrated by the .metrics file from MarkDuplicates getting deleted as an intermediate file, so I set
isIntermediate=false for that step in the DataProcessingPipeline. But now I'm getting tired of manually deleting the intermediate bams.
So my request is, could that field be changed from an @Output to an @Argument? This would be on line 50 of
org.broadinstitute.sting.queue.extensions.picard.MarkDuplicates.scala. I also made that a required field in my local copy, since it is required to run the Picard tool.
A similar but opposite problem is that the bai file from the IndelRealigner step is not deleted - but that looks like it would require either special handling for that walker in Queue or for the index file to be an argument to the Java walker. Neither is a particularly appealing solution.