Fix code style warnings

...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala

...umc/sasc/biopet/extensions/picard/BedToIntervalList.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

...asc/biopet/extensions/picard/CollectMultipleMetrics.scala

.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala

.../biopet/extensions/picard/CollectTargetedPcrMetrics.scala

...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala

...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala

.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala

...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala

.../scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala

.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala

.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala

...ala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala

.../lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala

.../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala