Change outputDir to File

...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

.../nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala

.../sasc/biopet/extensions/gatk/RealignerTargetCreator.scala

.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

...sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

...src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala

...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala

...c/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

...mc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala

...et/extensions/picard/CollectAlignmentSummaryMetrics.scala

.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala