Added Sage pipeline

biopet-framework/examples/sage.json

biopet-framework/pom.xml

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

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

.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

...rc/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala

.../main/scala/nl/lumc/sasc/biopet/scripts/prefixFastq.scala

...rc/main/scripts/nl/lumc/sasc/biopet/scripts/bed_squish.py

...c/main/scripts/nl/lumc/sasc/biopet/scripts/prefixFastq.py