Commit 7696695b authored 9 years ago by Peter van 't Hof

Merge remote-tracking branch 'remotes/origin/develop' into fix-shiva_fails

Conflicts:
	public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

parents 62a99234 8c42e046

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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 1 addition, 1 deletion

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala 19 additions, 15 deletions

...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala 9 additions, 11 deletions

.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala 2 additions, 2 deletions

.../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala 3 additions, 3 deletions

...la/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala 1 addition, 1 deletion

...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala 4 additions, 2 deletions

...in/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala 55 additions, 0 deletions

...umc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala 186 additions, 0 deletions

.../scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
public/gears/pom.xml 4 additions, 1 deletion

public/gears/pom.xml
public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp 38 additions, 0 deletions

...ources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp 69 additions, 0 deletions

...ces/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/report/ext/js/gears.js 341 additions, 0 deletions

...l/lumc/sasc/biopet/pipelines/gears/report/ext/js/gears.js
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala 108 additions, 274 deletions

...ain/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala 35 additions, 0 deletions

...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala 137 additions, 0 deletions

...scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
public/mapping/pom.xml 5 additions, 0 deletions

public/mapping/pom.xml
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala 13 additions, 3 deletions

...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala 11 additions, 2 deletions

...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala 9 additions, 1 deletion

...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

with 1050 additions and 316 deletions

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