Added scala files to jar and added a main class for each pipeline

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

flexiprep/nbactions.xml

flexiprep/pom.xml

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

gatk/nbactions.xml

gatk/pom.xml

...c/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala

mapping/nbactions.xml

mapping/pom.xml

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