From 9aad81a397acd520b2d2ae13c9e91dd71f325131 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 8 Nov 2014 19:40:41 +0100
Subject: [PATCH] Fix memory
---
.../scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index ea22e61d2..8a4140d1c 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -15,7 +15,7 @@ import scala.collection.SortedMap
import scala.collection.mutable.{ Map, Set }
import nl.lumc.sasc.biopet.core.config.Configurable
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 {
javaMainClass = getClass.getName
@@ -23,12 +23,14 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction
@Input(doc = "Input vcf files", shortName = "input", required = true)
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 = _
- @Argument
var reference: File = config("reference")
+ override val defaultVmem = "8G"
+ memoryLimit = Option(4)
+
override def commandLine = super.commandLine +
repeat("-I", input) +
required("-o", output) +
--
GitLab