Switch to fifo pipes

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

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

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

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

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

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

...cala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala

...ain/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala