Commit 9aad81a3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix memory

parent bc3e6582
...@@ -15,7 +15,7 @@ import scala.collection.SortedMap ...@@ -15,7 +15,7 @@ import scala.collection.SortedMap
import scala.collection.mutable.{ Map, Set } import scala.collection.mutable.{ Map, Set }
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import scala.collection.JavaConversions._ import scala.collection.JavaConversions._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument } import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction { class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName javaMainClass = getClass.getName
...@@ -23,12 +23,14 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction ...@@ -23,12 +23,14 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction
@Input(doc = "Input vcf files", shortName = "input", required = true) @Input(doc = "Input vcf files", shortName = "input", required = true)
var input: List[File] = Nil var input: List[File] = Nil
@Output(doc = "Output fastq files", shortName = "output", required = true) @Output(doc = "Output vcf file", shortName = "output", required = true)
var output: File = _ var output: File = _
@Argument
var reference: File = config("reference") var reference: File = config("reference")
override val defaultVmem = "8G"
memoryLimit = Option(4)
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
repeat("-I", input) + repeat("-I", input) +
required("-o", output) + required("-o", output) +
......
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