Changed own vmem

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

@@ -97,10 +97,11 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
     if (jobOutputFile == null && firstOutput != null)
       jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
 
-    if (threads == 0) threads = getThreads(defaultThreads) + pipesJobs.map(_.threads).map(i => if (i == 0) 1 else i).sum
+    val ownThreads = getThreads(defaultThreads)
+    if (threads == 0) threads = ownThreads + pipesJobs.map(_.threads).map(i => if (i == 0) 1 else i).sum
     if (threads > 1) nCoresRequest = Option(threads)
 
-    _coreMemory = config("core_memory", default = defaultCoreMemory +
+    _coreMemory = config("core_memory", default = (defaultCoreMemory * (ownThreads.toDouble / this.threads.toDouble)) +
       pipesJobs.map(job => job.coreMemeory * (job.threads.toDouble / this.threads.toDouble)).sum).asDouble +
       (0.5 * retry)
 

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.summary.{SummaryQScript, Summarizable}
+import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
 import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetPipe }
 import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle, Cutadapt }
 import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
@@ -43,11 +43,11 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
   override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
     clip match {
       case Some(job) => qscript.addSummarizable(job, s"clipping_$read")
-      case _ =>
+      case _         =>
     }
     trim match {
       case Some(job) => qscript.addSummarizable(job, s"trimming_$read")
-      case _ =>
+      case _         =>
     }
   }