Change vals to defs

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -15,15 +15,15 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
 
   jarFile = config("gatk_jar")
 
-  override val defaultCoreMemory = 4.0
+  override def defaultCoreMemory = 4.0
 
   if (config.contains("intervals")) intervals = config("intervals").asFileList
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
   if (config.contains("pedigree")) pedigree = config("pedigree")
 
-  override val versionRegex = """(.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """(.*)""".r
+  override def versionExitcode = List(0, 1)
   override def versionCommand = executable + " -jar " + jarFile + " -version"
 
   override def getVersion = super.getVersion.collect { case version => "Gatk " + version }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

@@ -33,11 +33,11 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   var deps: List[File] = Nil
 
   var threads = 0
-  val defaultThreads = 1
+  def defaultThreads = 1
 
   var vmem: Option[String] = config("vmem")
-  protected val defaultCoreMemory: Double = 1.0
-  protected val defaultVmemFactor: Double = 1.4
+  protected def defaultCoreMemory: Double = 1.0
+  protected def defaultVmemFactor: Double = 1.4
   var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
 
   var residentFactor: Double = config("resident_factor", default = 1.2)
@@ -151,10 +151,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   protected def versionCommand: String = null
 
   /** Regex to get version from version command output */
-  protected val versionRegex: Regex = null
+  protected def versionRegex: Regex = null
 
   /** Allowed exit codes for the version command */
-  protected val versionExitcode = List(0)
+  protected def versionExitcode = List(0)
 
   /** Executes the version command */
   private[core] def getVersionInternal(): Option[String] = {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

@@ -25,7 +25,7 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
   javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
   javaGCTimeLimit = config("java_gc_timelimit")
 
-  override protected val defaultVmemFactor: Double = 2.0
+  override protected def defaultVmemFactor: Double = 2.0
 
   /** Constructs java opts, this adds scala threads */
   override def javaOpts = super.javaOpts +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -26,7 +26,7 @@ trait ReportBuilderExtension extends ToolCommandFuntion {
   /** Arguments that are passed on the commandline */
   var args: Map[String, String] = Map()
 
-  override val defaultCoreMemory = 3.0
+  override def defaultCoreMemory = 3.0
 
   override def beforeGraph: Unit = {
     super.beforeGraph

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

@@ -40,12 +40,12 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
   var output: File = null
 
   executable = config("exe", default = "bowtie", freeVar = false)
-  override val versionRegex = """.*[Vv]ersion:? (.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """.*[Vv]ersion:? (.*)""".r
+  override def versionExitcode = List(0, 1)
   override def versionCommand = executable + " --version"
 
-  override val defaultCoreMemory = 4.0
-  override val defaultThreads = 8
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 8
 
   var sam: Boolean = config("sam", default = true)
   var sam_RG: Option[String] = config("sam-RG")

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

@@ -30,10 +30,10 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "cufflinks")
 
   /** default threads */
-  override val defaultThreads = 8
+  override def defaultThreads = 8
 
   /** default vmem for cluster jobs */
-  override val defaultCoreMemory = 6.0
+  override def defaultCoreMemory = 6.0
 
   /** input file */
   @Input(doc = "Input file (SAM or BAM)", required = true)
@@ -184,9 +184,9 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
   /** do not contact server to check for update availability [FALSE] */
   var no_update_check: Boolean = config("no_update_check", default = false)
 
-  override val versionRegex = """cufflinks v(.*)""".r
+  override def versionRegex = """cufflinks v(.*)""".r
   override def versionCommand = executable
-  override val versionExitcode = List(0, 1)
+  override def versionExitcode = List(0, 1)
 
   def cmdLine =
     required(executable) +

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

@@ -117,9 +117,9 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction {
   /** Disable SCV correction */
   var no_scv_correction: Boolean = config("no_scv_correction", default = false)
 
-  override val versionRegex = """cuffquant v(.*)""".r
+  override def versionRegex = """cuffquant v(.*)""".r
   override def versionCommand = executable
-  override val versionExitcode = List(0, 1)
+  override def versionExitcode = List(0, 1)
 
   def cmdLine =
     required(executable) +

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

@@ -40,7 +40,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
 
   executable = config("exe", default = "cutadapt")
   override def versionCommand = executable + " --version"
-  override val versionRegex = """(.*)""".r
+  override def versionRegex = """(.*)""".r
 
   var default_clip_mode: String = config("default_clip_mode", default = "3")
   var opt_adapter: Set[String] = config("adapter", default = Nil)

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

@@ -48,9 +48,9 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   var nogroup: Boolean = config("nogroup", default = false)
   var extract: Boolean = config("extract", default = true)
 
-  override val versionRegex = """FastQC (.*)""".r
+  override def versionRegex = """FastQC (.*)""".r
   override def versionCommand = executable + " --version"
-  override val defaultThreads = 4
+  override def defaultThreads = 4
 
   /** Sets contaminants and adapters when not yet set */
   override def beforeGraph {

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

@@ -39,7 +39,7 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
   var haplotypeLength: Option[Int] = config("haplotype_length")
 
   executable = config("exe", default = "freebayes")
-  override val versionRegex = """version:  (.*)""".r
+  override def versionRegex = """version:  (.*)""".r
   override def versionCommand = executable + " --version"
 
   override def beforeGraph: Unit = {

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

@@ -32,10 +32,10 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
   executable = config("exe", default = "gsnap", freeVar = false)
 
   /** default threads */
-  override val defaultThreads = 8
+  override def defaultThreads = 8
 
   /** default vmem for cluster jobs */
-  override val defaultCoreMemory = 10.0
+  override def defaultCoreMemory = 10.0
 
   /** input file */
   @Input(doc = "Input FASTQ file(s)", required = true) //var input: List[File] = _
@@ -329,7 +329,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
   /** value to put into read-group library (rg-pl) field */
   var read_group_platform: Option[String] = config("read_group_platform")
 
-  override val versionRegex = """.* version (.*)""".r
+  override def versionRegex = """.* version (.*)""".r
   override def versionCommand = executable + " --version"
 
   def cmdLine = {

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

@@ -29,7 +29,7 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "gzip")
 
-  override val versionRegex = """gzip (.*)""".r
+  override def versionRegex = """gzip (.*)""".r
   override def versionCommand = executable + " --version"
 
   def cmdLine = required(executable) + " -c " + repeat(input) + " > " + required(output)

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

@@ -69,7 +69,7 @@ class HtseqCount(val root: Configurable) extends BiopetCommandLineFunction {
   /** suppress progress report */
   var quiet: Boolean = config("quiet", default = false)
 
-  override val versionRegex = """.*, version (.*)\.""".r
+  override def versionRegex = """.*, version (.*)\.""".r
   override def versionCommand = executable + " --help"
 
   def cmdLine = {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala

@@ -33,7 +33,7 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "md5sum")
 
-  override val versionRegex = """md5sum \(GNU coreutils\) (.*)""".r
+  override def versionRegex = """md5sum \(GNU coreutils\) (.*)""".r
   override def versionCommand = executable + " --version"
 
   /** return commandline to execute */

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

@@ -33,8 +33,8 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
   var decomrpess = true
   var memory: Option[Int] = config("memory")
 
-  override val defaultCoreMemory = memory.getOrElse(1000).toDouble / 1000
-  override val defaultThreads = 2
+  override def defaultCoreMemory = memory.getOrElse(1000).toDouble / 1000
+  override def defaultThreads = 2
 
   override def beforeCmd {
     if (!memory.isEmpty) memory = Option(memory.get * threads)

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

@@ -27,9 +27,9 @@ import scalaz.std.boolean.option
  */
 class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
 
-  override val defaultThreads = 1
+  override def defaultThreads = 1
   override def versionCommand = executable + " -v"
-  override val versionRegex = """.*version ([\w\.]*) .*""".r
+  override def versionRegex = """.*version ([\w\.]*) .*""".r
 
   @Input(doc = "Input phy/fasta file", required = true)
   var input: File = _

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

@@ -58,7 +58,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
   var discardN: Boolean = config("discardN", default = false)
   var quiet: Boolean = config("quiet", default = false)
   var defaultQualityType: String = config("defaultqualitytype", default = "sanger")
-  override val versionRegex = """sickle version (.*)""".r
+  override def versionRegex = """sickle version (.*)""".r
   override def versionCommand = executable + " --version"
 
   /** Sets qualityType is still empty */

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

@@ -60,12 +60,12 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction with Refe
   var logfile: Option[String] = config("logfile")
 
   executable = config("exe", default = "stampy.py", freeVar = false)
-  override val versionRegex = """stampy v(.*) \(.*\), .*""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """stampy v(.*) \(.*\), .*""".r
+  override def versionExitcode = List(0, 1)
 
   /// Stampy uses approx factor 1.1 times the size of the genome in memory.
-  override val defaultCoreMemory = 4.0
-  override val defaultThreads = 8
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 8
 
   override def versionCommand = executable + " --help"
 

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

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

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

@@ -60,8 +60,8 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "tabix")
 
   override def versionCommand = executable
-  override val versionRegex = """Version: (.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """Version: (.*)""".r
+  override def versionExitcode = List(0, 1)
 
   /** Formats that tabix can handle */
   private val validFormats: Set[String] = Set("gff", "bed", "sam", "vcf", "psltbl")

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

@@ -28,12 +28,12 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "tophat", freeVar = false)
 
-  override val versionRegex = """TopHat v(.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """TopHat v(.*)""".r
+  override def versionExitcode = List(0, 1)
   override def versionCommand = executable + " --version"
 
-  override val defaultCoreMemory = 4.0
-  override val defaultThreads = 8
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 8
 
   @Input(doc = "FastQ file(s) R1", shortName = "R1")
   var R1: List[File] = List.empty[File]

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

@@ -36,7 +36,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   @Output(doc = "output file", required = true)
   var output: File = null
 
-  override val versionRegex = """version (\d*)""".r
+  override def versionRegex = """version (\d*)""".r
   override def versionCommand = executable + " " + vep_script + " --help"
 
   //Boolean vars
@@ -134,7 +134,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   var cache_region_size: Option[String] = config("cache_region_size")
 
   // Numeric args
-  override val defaultThreads: Int = config("fork", default = 2)
+  override def defaultThreads: Int = config("fork", default = 2)
   var cache_version: Option[Int] = config("cache_version")
   var freq_freq: Option[Float] = config("freq_freq")
   var port: Option[Int] = config("port")

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

@@ -30,7 +30,7 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "zcat")
 
-  override val versionRegex = """zcat \(gzip\) (.*)""".r
+  override def versionRegex = """zcat \(gzip\) (.*)""".r
   override def versionCommand = executable + " --version"
 
   /** Returns command to execute */

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

@@ -21,6 +21,6 @@ abstract class Bcftools extends BiopetCommandLineFunction {
   override def subPath = "bcftools" :: super.subPath
   executable = config("exe", default = "bcftools")
   override def versionCommand = executable
-  override val versionRegex = """Version: (.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """Version: (.*)""".r
+  override def versionExitcode = List(0, 1)
 }
\ No newline at end of file

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

@@ -22,5 +22,5 @@ abstract class Bedtools extends BiopetCommandLineFunction {
   override def subPath = "bedtools" :: super.subPath
   executable = config("exe", default = "bedtools", submodule = "bedtools")
   override def versionCommand = executable + " --version"
-  override val versionRegex = """bedtools (.*)""".r
+  override def versionRegex = """bedtools (.*)""".r
 }
\ No newline at end of file

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 defaultCoreMemory = 4.0
+  override def defaultCoreMemory = 4.0
 
   /** Returns command to execute */
   def cmdLine = required(executable) + required("coverage") +

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

@@ -9,10 +9,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "breakdancer-max", freeVar = false)
 
-  override val defaultThreads = 1 // breakdancer can only work on 1 single thread
+  override def defaultThreads = 1 // breakdancer can only work on 1 single thread
 
-  override val versionRegex = """.*[Vv]ersion:? (.*)""".r
-  override val versionExitcode = List(1)
+  override def versionRegex = """.*[Vv]ersion:? (.*)""".r
+  override def versionExitcode = List(1)
   override def versionCommand = executable
 
   @Input(doc = "The breakdancer configuration file")

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

@@ -25,7 +25,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 abstract class Bwa extends BiopetCommandLineFunction {
   override def subPath = "bwa" :: super.subPath
   executable = config("exe", default = "bwa")
-  override val versionRegex = """Version: (.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """Version: (.*)""".r
+  override def versionExitcode = List(0, 1)
   override def versionCommand = executable
 }

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

@@ -61,8 +61,8 @@ class BwaAln(val root: Configurable) extends Bwa with Reference {
   var n2: Boolean = config("2", default = false)
   var Y: Boolean = config("Y", default = false)
 
-  override val defaultCoreMemory = 4.0
-  override val defaultThreads = 8
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 8
 
   override def beforeGraph {
     super.beforeGraph

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

@@ -69,8 +69,8 @@ class BwaMem(val root: Configurable) extends Bwa with Reference {
   var Y: Boolean = config("Y", default = false)
   var I: Option[String] = config("I")
 
-  override val defaultCoreMemory = 4.0
-  override val defaultThreads = 8
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 8
 
   override def beforeGraph {
     super.beforeGraph

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

@@ -11,11 +11,11 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
 
   private lazy val versionexecutable: File = config("version_exe", default = (new File(executable).getParent + "/ctk-version"))
 
-  override val defaultThreads = 8
+  override def defaultThreads = 8
 
   override def versionCommand = versionexecutable.getAbsolutePath
-  override val versionRegex = """(.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """(.*)""".r
+  override def versionExitcode = List(0, 1)
 
   @Input(doc = "Input file (bam)")
   var input: File = _

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

@@ -22,12 +22,12 @@ abstract class Conifer extends PythonCommandLineFunction {
   override def subPath = "conifer" :: super.subPath
   //  executable = config("exe", default = "conifer")
   setPythonScript(config("script", default = "conifer"))
-  override val versionRegex = """(.*)""".r
-  override val versionExitcode = List(0)
+  override def versionRegex = """(.*)""".r
+  override def versionExitcode = List(0)
   override def versionCommand = executable + " " + python_script + " --version"
 
-  override val defaultCoreMemory = 5.0
-  override val defaultThreads = 1
+  override def defaultCoreMemory = 5.0
+  override def defaultThreads = 1
 
   def cmdLine = getPythonCommand
 

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

@@ -12,11 +12,11 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction {
 
   private lazy val versionexecutable: File = new File(executable)
 
-  override val defaultThreads = 1
+  override def defaultThreads = 1
 
   override def versionCommand = versionexecutable.getAbsolutePath
-  override val versionRegex = """DELLY \(Version: (.*)\)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """DELLY \(Version: (.*)\)""".r
+  override def versionExitcode = List(0, 1)
 
   @Input(doc = "Input file (bam)")
   var input: File = _

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

@@ -31,7 +31,7 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
 
   val analysisType: String
 
-  override val defaultCoreMemory = 3.0
+  override def defaultCoreMemory = 3.0
 
   @Input(required = true)
   var reference: File = null
@@ -48,8 +48,8 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
   @Input(required = false)
   var pedigree: List[File] = config("pedigree", default = Nil)
 
-  override val versionRegex = """(.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """(.*)""".r
+  override def versionExitcode = List(0, 1)
   override def versionCommand = executable + " -jar " + jarFile + " -version"
 
   override def getVersion = super.getVersion.collect { case version => "Gatk " + version }

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

@@ -25,6 +25,6 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 abstract class IGVTools extends BiopetCommandLineFunction {
   executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
   override def versionCommand = executable + " version"
-  override val versionRegex = """IGV Version:? ([\w\.]*) .*""".r
-  override val versionExitcode = List(0)
+  override def versionRegex = """IGV Version:? ([\w\.]*) .*""".r
+  override def versionExitcode = List(0)
 }
\ No newline at end of file

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 defaultCoreMemory = 4.0
+  override def defaultCoreMemory = 4.0
 
   override def beforeGraph {
     super.beforeGraph

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

@@ -51,11 +51,11 @@ class Kraken(val root: Configurable) extends BiopetCommandLineFunction {
   var paired: Boolean = config("paired", default = false)
 
   executable = config("exe", default = "kraken")
-  override val versionRegex = """Kraken version ([\d\w\-\.]+)\n.*""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """Kraken version ([\d\w\-\.]+)\n.*""".r
+  override def versionExitcode = List(0, 1)
 
-  override val defaultCoreMemory = 8.0
-  override val defaultThreads = 4
+  override def defaultCoreMemory = 8.0
+  override def defaultThreads = 4
 
   override def versionCommand = executable + " --version"
 

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

@@ -26,11 +26,11 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 class KrakenReport(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "kraken-report")
-  override val versionRegex = """Kraken version (.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """Kraken version (.*)""".r
+  override def versionExitcode = List(0, 1)
 
-  override val defaultCoreMemory = 4.0
-  override val defaultThreads = 1
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 1
 
   override def versionCommand = new File(new File(executable).getParent, "kraken").getAbsolutePath + " --version"
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala

@@ -25,6 +25,6 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 abstract class Macs2 extends BiopetCommandLineFunction {
   executable = config("exe", default = "macs2", submodule = "macs2", freeVar = false)
   override def versionCommand = executable + " --version"
-  override val versionRegex = """macs2 (.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """macs2 (.*)""".r
+  override def versionExitcode = List(0, 1)
 }

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

@@ -15,7 +15,7 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
 
   javaMainClass = new picard.analysis.CollectMultipleMetrics().getClass.getName
 
-  override val defaultCoreMemory = 6.0
+  override def defaultCoreMemory = 6.0
 
   @Input(doc = "The input SAM or BAM files to analyze", required = true)
   var input: File = null

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

@@ -58,10 +58,10 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
     if (jarFile != null) executable + " -cp " + jarFile + " " + javaMainClass + " -h"
     else null
   }
-  override val versionRegex = """Version: (.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """Version: (.*)""".r
+  override def versionExitcode = List(0, 1)
 
-  override val defaultCoreMemory = 3.0
+  override def defaultCoreMemory = 3.0
 
   override def getVersion = {
     if (jarFile == null) Picard.getBiopetPicardVersion

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

@@ -23,11 +23,11 @@ import java.io.File
 class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "pindel", freeVar = false)
 
-  override val defaultCoreMemory = 5.0
-  override val defaultThreads = 8
+  override def defaultCoreMemory = 5.0
+  override def defaultThreads = 8
 
-  override val versionRegex = """Pindel version:? (.*)""".r
-  override val versionExitcode = List(1)
+  override def versionRegex = """Pindel version:? (.*)""".r
+  override def versionExitcode = List(1)
   override def versionCommand = executable
 
   @Input(doc = "The pindel configuration file")

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

@@ -19,13 +19,13 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 /** General Sambamba extension */
 abstract class Sambamba extends BiopetCommandLineFunction {
-  override val defaultCoreMemory = 2.0
-  override val defaultThreads = 2
+  override def defaultCoreMemory = 2.0
+  override def defaultThreads = 2
 
   override def subPath = "sambamba" :: super.subPath
 
   executable = config("exe", default = "sambamba", freeVar = false)
   override def versionCommand = executable
-  override val versionRegex = """sambamba v(.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """sambamba v(.*)""".r
+  override def versionExitcode = List(0, 1)
 }
\ No newline at end of file

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

@@ -21,7 +21,7 @@ import java.io.File
 
 /** Extension for sambemba flagstat  */
 class SambambaFlagstat(val root: Configurable) extends Sambamba {
-  override val defaultThreads = 2
+  override def defaultThreads = 2
 
   @Input(doc = "Bam File")
   var input: File = _

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

@@ -21,7 +21,7 @@ import java.io.File
 
 /** Extension for sambemba index  */