Tweaking setting after testing

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

@@ -37,13 +37,11 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
 
   var vmem: Option[String] = config("vmem")
   protected val defaultCoreMemory: Double = 1.0
-  var vmemFactor: Double = config("vmem_factor", default =
-    this match {
-      case _: BiopetJavaCommandLineFunction => 2.5
-      case _                                => 1.5
-    })
+  var vmemFactor: Double = config("vmem_factor", default = 1.5)
+
+  var ressFactor: Double = config("vmem_factor", default = 1.2)
 
-  private var coreMemory: Double = config("core_memory", default = defaultCoreMemory)
+  private var coreMemory: Double = _
 
   var executable: String = _
 
@@ -65,25 +63,29 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     if (threads == 0) threads = getThreads(defaultThreads)
     if (threads > 1) nCoresRequest = Option(threads)
 
-    if (memoryLimit.isEmpty) memoryLimit = Some(coreMemory * threads)
+    coreMemory = config("core_memory", default = defaultCoreMemory).asDouble + (0.5 * retry)
+
+    if (config.contains("memory_limit")) memoryLimit = config("memory_limit")
+    else memoryLimit = Some(coreMemory * threads)
 
-    if (vmem.isEmpty) vmem = Some((defaultCoreMemory * vmemFactor) + "G")
+    if (config.contains("resident_limit")) memoryLimit = config("resident_limit")
+    else residentLimit = Some((coreMemory + (0.5 * retry)) * ressFactor)
+
+    if (!config.contains("vmem")) vmem = Some((coreMemory * (vmemFactor + (0.5 * retry))) + "G")
     if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
     jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
 
     super.freezeFieldValues()
   }
 
+  var retry = 0
+
   override def setupRetry(): Unit = {
     super.setupRetry()
+    if (vmem.isDefined) jobResourceRequests = jobResourceRequests.filterNot(_.contains("h_vmem="))
     logger.info("Auto raise memory on retry")
-    coreMemory += 1.0
-    vmemFactor += 0.5
-    memoryLimit = Some(coreMemory * threads)
-
-    if (vmem.isDefined) jobResourceRequests = jobResourceRequests.filter(_ != "h_vmem=" + vmem.get)
-    vmem = Some((defaultCoreMemory * vmemFactor) + "G")
-    jobResourceRequests :+= "h_vmem=" + vmem.get
+    retry += 1
+    this.freeze()
   }
 
   /** can override this value is executable may not be converted to CanonicalPath */