Fixing dir names

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

@@ -104,7 +104,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       case _               =>
     }
 
-    val logDir = new File(outputDir, ".log" + File.separator + BiopetQCommandLine.timestamp)
+    val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase)
 
     if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
       globalConfig.writeReport(new File(logDir, "config"))

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

@@ -77,7 +77,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
     val pipelineConfig = globalConfig.map.getOrElse(pipelineName, Map()).asInstanceOf[Map[String, Any]]
     val pipelineOutputDir = new File(globalConfig.map.getOrElse("output_dir", pipelineConfig.getOrElse("output_dir", "./")).toString)
     BiopetQScript.checkOutputDir(pipelineOutputDir)
-    val logDir: File = new File(pipelineOutputDir, ".log" + File.separator + BiopetQCommandLine.timestamp)
+    val logDir: File = new File(pipelineOutputDir, ".log" + File.separator + pipelineName + "." + BiopetQCommandLine.timestamp)
     logDir.mkdirs()
 
     val logFile = new File(logDir, "biopet.log")

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

@@ -50,6 +50,7 @@ object WriteDependencies extends Logging with Configurable {
    * @param outputDir
    */
   def writeDependencies(functions: Seq[QFunction], outputDir: File): Unit = {
+    outputDir.mkdirs()
     logger.info("Start calculating dependencies")
 
     val errorOnMissingInput: Boolean = config("error_on_missing_input", false)