Using CRAM files in Picard SamToFastq with Queue
I'm trying to convert CRAM files to FASTQ format with SamToFastq as part of a pipeline I have written in a Queue script. Is there any parameter for passing a reference file in the SamToFastq Queue module? I didn't see any such parameter in SamToFastq.scala, PicardBamFunction.scala, or JavaCommandLineFunction.scala. I couldn't find anything on the forum, and I tried a bunch of different things by guessing, but didn't have any luck. If there is no parameter to use a reference file in a Queue script for Picard tools, is there any sort of workaround (e.g., environment variable that Picard will pick up on)?