I was trying to run the method rnaseq-germline-snps-indels, cloned from the workspace help-gatk/rna-seq-germline-snps-indels, on some of my RNAseq samples, and all except one failed at the RNAseq.SplitNCigarReads step. The stderr files show the following error message:
"An error occurred because you did not provide enough memory to run this program. You can use the -Xmx argument (before the -jar argument) to adjust the maximum heap size provided to Java. Note that this is a JVM argument, not a GATK argument."
I don't see any variable named Xmx in the inputs of the method configuration, so I suppose the error message is asking to modify the WDL file. Can you please tell me which line(s) of the WDL file need to be edited? And how much memory would be enough to run this program (my largest bam file is 12GB)?