Merge branch 'feature-sanity_check_outputdir' into 'develop'

Added sanity checks for outputDir

fixing: BIOPET-406

See merge request !470

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

@@ -38,6 +38,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
     if (config.contains("output_dir", path = Nil)) config("output_dir", path = Nil).asFile
     else new File(".")
   }
+  require(outputDir.canRead, s"No premision to read outputdir: $outputDir")
+  require(outputDir.canWrite, s"No premision to read outputdir: $outputDir")
 
   @Argument(doc = "Disable all scatters", shortName = "DSC", required = false)
   var disableScatter: Boolean = false
@@ -67,6 +69,9 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
   final def script() {
     outputDir = config("output_dir")
     outputDir = outputDir.getAbsoluteFile
+
+    BiopetQScript.checkOutputDir(outputDir)
+
     init()
     biopetScript()
     logger.info("Biopet script done")
@@ -153,4 +158,13 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
 
 object BiopetQScript {
   case class InputFile(file: File, md5: Option[String] = None)
+
+  def checkOutputDir(outputDir: File): Unit = {
+    // Sanity checks
+    require(outputDir.getParentFile.canRead, s"No premision to read parent of outputdir: ${outputDir.getParentFile}")
+    require(outputDir.getParentFile.canWrite, s"No premision to write parent of outputdir: ${outputDir.getParentFile}")
+    outputDir.mkdir()
+    require(outputDir.canRead, s"No premision to read outputdir: $outputDir")
+    require(outputDir.canWrite, s"No premision to write outputdir: $outputDir")
+  }
 }

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

@@ -77,6 +77,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
       val pipelineName = this.getClass.getSimpleName.toLowerCase.split("""\$""").head
       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")
       logDir.mkdirs()
       new File(logDir, "biopet." + BiopetQCommandLine.timestamp + ".log")