I have been using a workflow to analyze sequencing data has previously worked well, but recently the workflow has failed at steps using GATK tools. The GATK tools work fine when used individually, but when compiled into a workflow the 'false' settings are changed to 'true', which then causes an error.
For example in the Unified Genotyper tool, I set the "Disable experimental low-memory sharding functionality" to 'false'. When run as part of the workflow, this option is switched to 'true' and leads to an error "ERROR MESSAGE: Argument with name 'disable_experimental_low_memory_sharding' isn't defined." I can fix this issue by running each tool individually and unchecking the boxes, but that defeats the purpose of the workflow. Does anyone know what would be causing this problem? Is it a Galaxy issue or a GATK issue?