Fix threads allocation to GSNAP, TopHat, and Cufflinks wrappers

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

@@ -67,9 +67,6 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
   /** write all output files to this directory [./] */
   var output_dir: File = config("output_dir", default = new File("."))
 
-  /** number of threads used during analysis [1] */
-  var num_threads: Option[Int] = config("num_threads")
-
   /** value of random number generator seed [0] */
   var seed: Option[Int] = config("seed")
 
@@ -191,10 +188,6 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
   override def versionCommand = executable
   override val versionExitcode = List(0, 1)
 
-  override def beforeGraph: Unit = {
-    threads = num_threads.getOrElse(1)
-  }
-
   def cmdLine =
     required(executable) +
       required("--output-dir", output_dir) +

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

@@ -176,9 +176,6 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
   /** use this runlength iit file to resolve concordant multiple results */
   var use_runlength: Option[String] = config("use_runlength")
 
-  /** number of worker threads */
-  var nthreads: Option[Int] = config("nthreads")
-
   /** cases to use gmap for complex alignments containing multiple splices or indels */
   var gmap_mode: Option[String] = config("gmap_mode")
 

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

@@ -134,8 +134,6 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
 
   var library_type: Option[String] = config("library_type")
 
-  var num_threads: Option[Int] = config("num_threads")
-
   var resume: Option[String] = config("resume")
 
   var GTF: Option[String] = config("GTF")
@@ -266,10 +264,6 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
 
   var rg_platform: Option[String] = config("rg_platform")
 
-  override def beforeGraph: Unit = {
-    threads = num_threads.getOrElse(1)
-  }
-
   def cmdLine: String = required(executable) +
     optional("-o", output_dir) +
     conditional(bowtie1, "--bowtie1") +