Added init version of dependency debug mode

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

@@ -102,6 +102,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
       case _ => reportClass.foreach(add(_))
     }
 
+    if (logger.isDebugEnabled) WriteDependencies.writeDependencies(functions, new File(outputDir, s".log/${qSettings.runName}.deps.json"))
+
     Logging.checkErrors()
   }
 

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

+package nl.lumc.sasc.biopet.core
+
+import java.io.{File, PrintWriter}
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.queue.function.{CommandLineFunction, QFunction}
+import scala.collection.mutable
+
+/**
+  * Created by pjvanthof on 06/11/15.
+  */
+object WriteDependencies {
+  val functionNames: mutable.Map[QFunction, String] = mutable.Map()
+
+  def createFunctionNames(functions: Seq[QFunction]): Unit = {
+    val cache: mutable.Map[String, Int] = mutable.Map()
+    for (function <- functions) {
+      val baseName = function match {
+        case f: BiopetCommandLineFunction => f.configName
+        case f => f.getClass.getSimpleName
+      }
+      cache += baseName -> (cache.getOrElse(baseName, 0) + 1)
+      functionNames += function -> (s"$baseName-${cache(baseName)}")
+    }
+  }
+
+  def writeDependencies(functions: Seq[QFunction], outputFile: File): Unit = {
+    createFunctionNames(functions)
+    val writer = new PrintWriter(outputFile)
+    val jobs = functionNames.map { case (f, name) => name -> Map("command" -> (f match {
+      case cmd: CommandLineFunction => cmd.commandLine
+      case _ => None
+    }), "intermediate" -> f.isIntermediate) }
+
+    writer.println(ConfigUtils.mapToJson(jobs.toMap).spaces2)
+    writer.close()
+  }
+
+}