Aggregate threads and corememory for pipes

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

@@ -84,16 +84,19 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
     val firstOutput = try {
       this.firstOutput
     } catch {
-      case e:NullPointerException => null
+      case e: NullPointerException => null
     }
 
+    pipesJobs.foreach(_.beforeGraph())
+    pipesJobs.foreach(_.internalBeforeGraph())
+
     if (jobOutputFile == null && firstOutput != null)
       jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
 
-    if (threads == 0) threads = getThreads(defaultThreads)
+    if (threads == 0) threads = getThreads(defaultThreads) + pipesJobs.map(_.threads).sum
     if (threads > 1) nCoresRequest = Option(threads)
 
-    _coreMemory = config("core_memory", default = defaultCoreMemory).asDouble + (0.5 * retry)
+    _coreMemory = config("core_memory", default = defaultCoreMemory + pipesJobs.map(_.coreMemeory).sum).asDouble + (0.5 * retry)
 
     if (config.contains("memory_limit")) memoryLimit = config("memory_limit")
     else memoryLimit = Some(_coreMemory * threads)
@@ -311,6 +314,8 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
     cmd
   }
 
+  private[core] var pipesJobs: List[BiopetCommandLineFunction] = Nil
+
   def requiredInput(prefix: String, arg: Either[File, BiopetCommandLineFunction]): String = {
     arg match {
       case Left(file) => {
@@ -319,11 +324,7 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
       }
       case Right(cmd) => {
         cmd._outputAsStdout = true
-        cmd.beforeGraph()
-        cmd.internalBeforeGraph()
-        this.beforeGraph()
-        this.internalBeforeGraph()
-        this.threads += cmd.threads
+        pipesJobs :+= cmd
         try {
           if (cmd.outputs != null) outputFiles ++= cmd.outputs
           if (cmd.inputs != null) deps ++= cmd.inputs
@@ -343,11 +344,7 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
       }
       case Right(cmd) => {
         cmd._inputAsStdin = true
-        cmd.beforeGraph()
-        cmd.internalBeforeGraph()
-        this.beforeGraph()
-        this.internalBeforeGraph()
-        this.threads += cmd.threads
+        pipesJobs :+= cmd
         try {
           if (cmd.outputs != null) outputFiles ++= cmd.outputs
           if (cmd.inputs != null) deps ++= cmd.inputs

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

@@ -26,10 +26,10 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
     case e: Exception => Nil
   }
 
+  pipesJobs :::= commands
+
   override def beforeGraph() {
     super.beforeGraph()
-    commands.foreach(_.beforeGraph())
-    commands.foreach(_.internalBeforeGraph())
 
     stdoutFile = stdoutFile.map(_.getAbsoluteFile)
     stdinFile = stdinFile.map(_.getAbsoluteFile)
@@ -45,14 +45,8 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
     require(inputOutput.isEmpty, "File found as input and output in the same job, files: " + inputOutput.mkString(", "))
   }
 
-  override def defaultCoreMemory = {
-    (for (command <- commands) yield {
-      val threads = command.getThreads(command.defaultThreads)
-      val totalThreads = defaultThreads
-      (threads.toDouble / totalThreads.toDouble) * command.defaultCoreMemory
-    }).sum
-  }
-  override def defaultThreads = commands.map(c => c.getThreads(c.defaultThreads)).sum
+  override def defaultCoreMemory = 0.0
+  override def defaultThreads = 0
 
   val root: Configurable = commands.head.root
   override def configName = commands.map(_.configName).mkString("-")