Added GatkPipeline, finaly replacement for "Gatk" pipeline
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- gatk-pipeline/.gitignore 1 addition, 0 deletionsgatk-pipeline/.gitignore
- gatk-pipeline/README.md 8 additions, 0 deletionsgatk-pipeline/README.md
- gatk-pipeline/examples/test.json 48 additions, 0 deletionsgatk-pipeline/examples/test.json
- gatk-pipeline/pom.xml 155 additions, 0 deletionsgatk-pipeline/pom.xml
- gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala 231 additions, 0 deletions...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
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