Commit fb215ab1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix bug on vmem

parent c008141f
......@@ -15,13 +15,11 @@
*/
package nl.lumc.sasc.biopet.core
//import java.io.BufferedInputStream
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QException
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
//import scala.io.Source
import scala.sys.process.{ Process, ProcessLogger }
import scala.util.matching.Regex
import java.io.FileInputStream
......@@ -62,7 +60,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
vmem = config("vmem")
if (vmem.isEmpty && defaultVmem.nonEmpty) vmem = Some(defaultVmem)
}
if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
super.freezeFieldValues()
......
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