Merge branch 'feature-gears' into 'develop'
Feature gears (metagenomics) Metagenomics pipeline, start from bam or from FastQ files. Dependencies: - Sambamba (v0.5.1+) - Kraken See merge request !168
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- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala 92 additions, 0 deletions.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala 52 additions, 0 deletions.../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala 47 additions, 0 deletions...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
- public/biopet-public-package/pom.xml 5 additions, 0 deletionspublic/biopet-public-package/pom.xml
- public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala 2 additions, 1 deletion...ala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
- public/gears/.gitignore 1 addition, 0 deletionspublic/gears/.gitignore
- public/gears/pom.xml 57 additions, 0 deletionspublic/gears/pom.xml
- public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala 27 additions, 0 deletions...ain/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
- public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTrait.scala 330 additions, 0 deletions...cala/nl/lumc/sasc/biopet/pipelines/gears/GearsTrait.scala
- public/gears/src/test/resources/log4j.properties 25 additions, 0 deletionspublic/gears/src/test/resources/log4j.properties
- public/pom.xml 2 additions, 0 deletionspublic/pom.xml
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