Small changes on config setup

...ework/src/main/java/nl/lumc/sasc/biopet/core/Config.scala

...work/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala

...k/src/main/java/nl/lumc/sasc/biopet/wrappers/Fastqc.scala

...k/src/main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala

...ork/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala

...ork/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala

flexiprep/examples/test.json

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

...umc/sasc/biopet/pipelines/flexiprep/FastqcToContams.scala

...mc/sasc/biopet/pipelines/flexiprep/FastqcToQualtype.scala