Fixing code warning from ide

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

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

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

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

...k/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

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

...scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala

...main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala

...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

...scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala

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

...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala

...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala