Fixing temp files

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala

@@ -22,6 +22,8 @@ import org.broadinstitute.gatk.queue.function.CommandLineFunction
  */
 trait CommandLineResources extends CommandLineFunction with Configurable {
 
+  lazy val maxThreads: Option[Int] = config("max_threads")
+
   def defaultThreads = 1
   final def threads = nCoresRequest match {
     case Some(i) => i
@@ -72,7 +74,6 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
    * @return number of threads
    */
   private def getThreads(default: Int): Int = {
-    val maxThreads: Option[Int] = config("maxthreads")
     val threads: Int = config("threads", default = default)
     maxThreads match {
       case Some(max) => if (max > threads) threads else max
@@ -120,6 +121,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
   protected def combineResources(commands: List[CommandLineResources]): Unit = {
     commands.foreach(_.setResources())
     nCoresRequest = Some(commands.map(_.threads).sum + threadsCorrection)
+    nCoresRequest.map(x => if (x > maxThreads.getOrElse(x)) maxThreads.getOrElse(x) else x)
 
     _coreMemory = commands.map(cmd => cmd.coreMemory * (cmd.threads.toDouble / threads.toDouble)).sum
     memoryLimit = Some(_coreMemory * threads)

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

@@ -135,6 +135,7 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
           }
           md5sum.input = file
           md5sum.output = new File(file.getParentFile, file.getName + ".md5")
+          md5sum.jobOutputFile = new File(file.getParentFile, s".${file.getName}.md5.md5sum.out")
 
           // Need to not write a md5 file outside the outputDir
           if (!file.getAbsolutePath.startsWith(outputDir.getAbsolutePath))

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -41,6 +41,8 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
   /** Make a final fastq files, by default only when flexiprep is the main pipeline */
   var keepQcFastqFiles: Boolean = config("keepQcFastqFiles", default = parent == null)
 
+  override def defaults = super.defaults ++ Map("max_threads" -> 4)
+
   /** Returns files to store in summary */
   def summaryFiles: Map[String, File] = {
     Map("input_R1" -> inputR1, "output_R1" -> fastqR1Qc) ++