Merge branch 'develop' into feature-copy_lib_summary

README.md

docs/about.md

docs/config.md

docs/examples/gentrap_example.json

docs/general/config.md

docs/license.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

protected/biopet-gatk-extensions/pom.xml

...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

.../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala