Commit 801ac09e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added default vmem

parent 4b5b6c56
package nl.lumc.sasc.biopet.core.apps
import java.io.BufferedInputStream
import java.io.File
import java.io.FileInputStream
import java.io.PrintWriter
import java.io.{BufferedInputStream, File, FileInputStream, PrintWriter}
import java.util.zip.GZIPInputStream
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import scala.io.Source
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.sting.commandline._
import org.broadinstitute.sting.commandline.{Input, Output}
class FastqSplitter(val root:Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = "nl.lumc.sasc.biopet.core.apps.FastqSplitter"
javaMainClass = getClass.getName
@Input(doc="Input fastq", shortName = "input", required = true)
var input: File = _
......@@ -19,6 +16,9 @@ class FastqSplitter(val root:Configurable) extends BiopetJavaCommandLineFunction
@Output(doc="Output fastq files", shortName="output", required = true)
var output: List[File] = Nil
override val defaultVmem = "8G"
memoryLimit = Option(4.0)
override def commandLine = super.commandLine + required(input) + repeat(output)
}
......
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