fix merge request issues

...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala

.../lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala

...in/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala

.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala

.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala

...sc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala

...sc/biopet/extensions/manwe/ManweDataSourcesDownload.scala

...c/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala

...c/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala

...c/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala

...l/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala

...pet/extensions/manwe/ManweSamplesAnnotateVariations.scala

...umc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala

.../sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala

.../sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala

.../lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala

.../lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala

...test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala

...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala