Remove BIOPET_CONFIG_SCATTER env value, change flag to disable scatters

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

@@ -6,6 +6,7 @@ import nl.lumc.sasc.biopet.core.config.{ Config, Configurable }
 import org.broadinstitute.gatk.utils.commandline.Argument
 import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.function.QFunction
+import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
 
 trait BiopetQScript extends Configurable {
 
@@ -15,8 +16,8 @@ trait BiopetQScript extends Configurable {
   @Argument(doc = "Output directory", fullName = "output_directory", shortName = "outDir", required = true)
   var outputDir: String = _
 
-  @Argument(doc = "Use scatter defaults, env value BIOPET_CONFIG_SCATTER", shortName = "SC", required = false)
-  var useScatterDefault: Boolean = false
+  @Argument(doc = "Disable all scatters", shortName = "DSC", required = false)
+  var disableScatterDefault: Boolean = false
 
   var outputFiles: Map[String, File] = Map()
 
@@ -28,10 +29,14 @@ trait BiopetQScript extends Configurable {
   var functions: Seq[QFunction]
 
   final def script() {
-    if (useScatterDefault) Config.global.loadDefaultScatterConfig
     if (!outputDir.endsWith("/")) outputDir += "/"
     init
     biopetScript
+
+    if (disableScatterDefault) for (function <- functions) function match {
+      case f: ScatterGatherableFunction => f.scatterCount = 1
+      case _                            =>
+    }
     for (function <- functions) function match {
       case f: BiopetCommandLineFunctionTrait => f.afterGraph
       case _                                 =>

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala

@@ -28,10 +28,6 @@ class Config(var map: Map[String, Any]) extends Logging {
     loadConfigEnv("BIOPET_CONFIG")
   }
 
-  def loadDefaultScatterConfig() {
-    loadConfigEnv("BIOPET_CONFIG_SCATTER")
-  }
-
   def loadConfigFile(configFile: File) {
     logger.debug("Jsonfile: " + configFile)
     val jsonText = scala.io.Source.fromFile(configFile).mkString