Merge with changes from develop

README.md

docs/developer/example-pipeline.md

docs/developer/example-tool.md

docs/developer/scaladocs.md

docs/general/config.md

docs/general/memory.md

docs/index.md

docs/pipelines/bam2wig.md

docs/pipelines/basty.md

docs/pipelines/carp.md

docs/pipelines/flexiprep.md

docs/pipelines/gears.md

docs/pipelines/gentrap.md

docs/pipelines/mapping.md

docs/pipelines/sage.md

docs/pipelines/shiva.md

docs/pipelines/toucan.md

docs/releasenotes/release_notes_0.6.0.md

mkdocs.yml

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala