Move config report

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

@@ -104,8 +104,10 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       case _               =>
     }
 
+    val logDir = new File(outputDir, ".log" + File.separator + BiopetQCommandLine.timestamp)
+
     if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
-      globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
+      globalConfig.writeReport(new File(logDir, "config"))
     else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, output directory cannot be created")
 
     logger.info("Checking input files")
@@ -126,7 +128,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
 
     if (!skipWriteDependencies) WriteDependencies.writeDependencies(
       functions,
-      new File(outputDir, ".log" + File.separator + BiopetQCommandLine.timestamp + File.separator + "graph"))
+      new File(logDir, "graph"))
 
     Logging.checkErrors()
     logger.info("Script complete without errors")

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala

@@ -189,7 +189,7 @@ class Config(protected var _map: Map[String, Any],
     } else ConfigValue(requestedIndex, null, null, freeVar)
   }
 
-  def writeReport(id: String, directory: File): Unit = {
+  def writeReport(directory: File): Unit = {
     directory.mkdirs()
 
     def convertIndexValuesToMap(input: List[(ConfigValueIndex, Any)], forceFreeVar: Option[Boolean] = None): Map[String, Any] = {
@@ -205,7 +205,7 @@ class Config(protected var _map: Map[String, Any],
     }
 
     def writeMapToJsonFile(map: Map[String, Any], name: String): Unit = {
-      val file = new File(directory, id + "." + name + ".json")
+      val file = new File(directory, name + ".json")
       val writer = new PrintWriter(file)
       writer.write(ConfigUtils.mapToJson(map).spaces2)
       writer.close()