The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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)?