Switch pipeline to reference module

protected/biopet-gatk-pipelines/src/test/resources/ref.dict

protected/biopet-gatk-pipelines/src/test/resources/ref.fa

...ected/biopet-gatk-pipelines/src/test/resources/ref.fa.fai

.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

public/carp/src/test/resources/ref.dict

public/carp/src/test/resources/ref.fa

public/carp/src/test/resources/ref.fa.fai

...t/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

public/mapping/src/test/resources/ref.dict

public/mapping/src/test/resources/ref.fa

public/mapping/src/test/resources/ref.fa.fai

...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

public/shiva/src/test/resources/ref.dict

public/shiva/src/test/resources/ref.fa

public/shiva/src/test/resources/ref.fa.fai

...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala