Change limits to coreMemory

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

@@ -44,7 +44,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   override val versionExitcode = List(0, 1)
   override def versionCommand = executable + " --version"
 
-  override val defaultVmem = "6G"
+  override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
   var sam: Boolean = config("sam", default = true)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala

@@ -33,7 +33,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
   override val defaultThreads = 8
 
   /** default vmem for cluster jobs */
-  override val defaultVmem = "8G"
+  override val defaultCoreMemory = 6.0
 
   /** input file */
   @Input(doc = "Input file (SAM or BAM)", required = true)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala

@@ -35,7 +35,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
   override val defaultThreads = 8
 
   /** default vmem for cluster jobs */
-  override val defaultVmem = "16G"
+  override val defaultCoreMemory = 10.0
 
   /** input file */
   @Input(doc = "Input FASTQ file(s)", required = true) //var input: List[File] = _

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala

@@ -33,7 +33,7 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
   var decomrpess = true
   var memory: Option[Int] = config("memory")
 
-  override val defaultVmem = (memory.getOrElse(1000) * 2 / 1000) + "G"
+  override val defaultCoreMemory = memory.getOrElse(1000).toDouble / 1000
   override val defaultThreads = 2
 
   override def beforeCmd {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala

@@ -36,7 +36,7 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
   protected var script: File = _
   protected var scriptName: String = _
   protected var arguments: ListBuffer[String] = ListBuffer()
-  override val defaultVmem: String = "4G"
+  override val defaultCoreMemory = 2.0
 
   executable = config("exe", default = "Rscript", submodule = "R")
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala

@@ -64,7 +64,7 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
   override val versionExitcode = List(0, 1)
 
   /// Stampy uses approx factor 1.1 times the size of the genome in memory.
-  override val defaultVmem = "4G"
+  override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
   override def versionCommand = executable + " --help"

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

@@ -63,7 +63,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
   var outFileNamePrefix: String = _
   var runThreadN: Option[Int] = config("runThreadN")
 
-  override val defaultVmem = "6G"
+  override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
   /** Sets output files for the graph */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala

@@ -32,7 +32,7 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
   override val versionExitcode = List(0, 1)
   override def versionCommand = executable + " --version"
 
-  override val defaultVmem = "6G"
+  override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
   @Input(doc = "FastQ file(s) R1", shortName = "R1")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

@@ -46,7 +46,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
     if (input.getName.endsWith(".bam")) inputTag = "-abam"
   }
 
-  override val defaultVmem = "6G"
+  override val defaultCoreMemory = 4.0
 
   /** Returns command to execute */
   def cmdLine = required(executable) + required("coverage") +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala

@@ -60,7 +60,7 @@ class BwaAln(val root: Configurable) extends Bwa {
   var n2: Boolean = config("2", default = false)
   var Y: Boolean = config("Y", default = false)
 
-  override val defaultVmem = "5G"
+  override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
   /** Returns command to execute */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

@@ -69,7 +69,7 @@ class BwaMem(val root: Configurable) extends Bwa {
   var Y: Boolean = config("Y", default = false)
   var I: Option[String] = config("I")
 
-  override val defaultVmem = "6G"
+  override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
   def cmdLine = {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala

@@ -26,7 +26,7 @@ abstract class Conifer extends PythonCommandLineFunction {
   override val versionExitcode = List(0)
   override def versionCommand = executable + " " + python_script + " --version"
 
-  override val defaultVmem = "8G"
+  override val defaultCoreMemory = 5.0
   override val defaultThreads = 1
 
   def cmdLine = getPythonCommand

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala

@@ -31,7 +31,7 @@ abstract class Gatk extends BiopetJavaCommandLineFunction {
 
   val analysisType: String
 
-  override val defaultVmem = "5G"
+  override val defaultCoreMemory = 3.0
 
   @Input(required = true)
   var reference: File = config("reference")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

@@ -59,7 +59,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
 
   var pairs: Boolean = config("pairs", default = false)
 
-  override val defaultVmem = "6G"
+  override val defaultCoreMemory = 4.0
 
   override def beforeGraph {
     super.beforeGraph

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

@@ -60,8 +60,7 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
   override val versionRegex = """Version: (.*)""".r
   override val versionExitcode = List(0, 1)
 
-  override val defaultVmem = "8G"
-  memoryLimit = Option(3.0)
+  override val defaultCoreMemory = 3.0
 
   override def commandLine = super.commandLine +
     required("TMP_DIR=" + jobTempDir) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala

@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 /** General Sambamba extension */
 abstract class Sambamba extends BiopetCommandLineFunction {
-  override val defaultVmem = "4G"
+  override val defaultCoreMemory = 2.0
   override val defaultThreads = 2
 
   override def subPath = "sambamba" :: super.subPath

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala

@@ -84,7 +84,7 @@ object BreakdancerConfig {
 class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "breakdancer-max", freeVar = false)
 
-  override val defaultVmem = "6G"
+  override val defaultCoreMemory = 4.0
   override val defaultThreads = 1 // breakdancer can only work on 1 single thread
 
   override val versionRegex = """.*[Vv]ersion:? (.*)""".r

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala

@@ -28,7 +28,7 @@ class Clever(val root: Configurable) extends BiopetCommandLineFunction {
 
   private lazy val versionexecutable: File = config("version_exe", default = (new File(executable).getParent + "/ctk-version"))
 
-  override val defaultVmem = "4G"
+  override val defaultCoreMemory = 3.0
   override val defaultThreads = 8
 
   override def versionCommand = versionexecutable.getAbsolutePath

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala

@@ -23,7 +23,7 @@ import java.io.File
 class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "pindel", freeVar = false)
 
-  override val defaultVmem = "8G"
+  override val defaultCoreMemory = 5.0
   override val defaultThreads = 8
 
   override val versionRegex = """Pindel version:? (.*)""".r

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala

@@ -29,7 +29,6 @@ abstract class Varscan extends BiopetJavaCommandLineFunction {
    * override val versionRegex = """VarScan v(.*)""".r
    */
 
-  override val defaultVmem = "8G"
-  memoryLimit = Option(3.0)
+  override val defaultCoreMemory = 5.0
 }