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Merge branch 'develop' into feature-confignamespace
Conflicts: public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
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- .gitignore 1 addition, 0 deletions.gitignore
- biopet-aggregate/pom.xml 1 addition, 0 deletionsbiopet-aggregate/pom.xml
- docs/general/config.md 2 additions, 2 deletionsdocs/general/config.md
- docs/pipelines/carp.md 46 additions, 2 deletionsdocs/pipelines/carp.md
- docs/pipelines/flexiprep.md 2 additions, 2 deletionsdocs/pipelines/flexiprep.md
- docs/pipelines/mapping.md 2 additions, 2 deletionsdocs/pipelines/mapping.md
- docs/pipelines/shiva.md 11 additions, 0 deletionsdocs/pipelines/shiva.md
- docs/pipelines/tinycap.md 109 additions, 0 deletionsdocs/pipelines/tinycap.md
- docs/releasenotes/release_notes_0.6.0.md 8 additions, 0 deletionsdocs/releasenotes/release_notes_0.6.0.md
- external-example/pom.xml 4 additions, 4 deletionsexternal-example/pom.xml
- mkdocs.yml 1 addition, 0 deletionsmkdocs.yml
- pom.xml 1 addition, 1 deletionpom.xml
- protected/biopet-gatk-extensions/pom.xml 1 addition, 1 deletionprotected/biopet-gatk-extensions/pom.xml
- protected/biopet-gatk-pipelines/pom.xml 1 addition, 1 deletionprotected/biopet-gatk-pipelines/pom.xml
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala 2 additions, 2 deletions...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala 5 additions, 0 deletions...iopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala 5 additions, 0 deletions...pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerGvcf.scala 5 additions, 0 deletions...t/pipelines/gatk/variantcallers/HaplotypeCallerGvcf.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala 5 additions, 0 deletions...opet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala 5 additions, 0 deletions...ipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala
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