Commit 109ff2b3 authored by bow's avatar bow
Browse files

Merge branch 'feature-gatk_jar' into 'develop'

Feature gatk jar

Added option for selecting jar file for gatk. Possible to tun older versions now

See merge request !50
parents 26d1fd82 bfd2bddb
......@@ -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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