Merge branch 'develop' into feature-report

docs/config.md

docs/general/config.md

docs/pipelines/bam2wig.md

docs/pipelines/basty.md

docs/pipelines/flexiprep.md

docs/pipelines/gentrap.md

docs/pipelines/mapping.md

docs/pipelines/sage.md

docs/pipelines/shiva.md

docs/pipelines/toucan.md

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

...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala

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

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

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