Commit bfd2bddb authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add gatk jar option

parent 26d1fd82
......@@ -6,6 +6,8 @@ import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
memoryLimit = Option(3)
if (config.contains("gatk_jar")) jarFile = config("gatk_jar")
override val defaultVmem = "7G"
if (config.contains("intervals", submodule = "gatk")) intervals = config("intervals", submodule = "gatk").getFileList
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