Merge remote-tracking branch 'origin/develop' into feature-input_files_checking
Conflicts: public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
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- README.md 8 additions, 8 deletionsREADME.md
- docs/general/requirements.md 17 additions, 0 deletionsdocs/general/requirements.md
- docs/index.md 90 additions, 1 deletiondocs/index.md
- docs/index.md 90 additions, 1 deletiondocs/index.md
- docs/tools/SamplesTsvToJson.md 1 addition, 1 deletiondocs/tools/SamplesTsvToJson.md
- mkdocs.yml 2 additions, 1 deletionmkdocs.yml
- pom.xml 1 addition, 1 deletionpom.xml
- protected/biopet-gatk-extensions/pom.xml 2 additions, 2 deletionsprotected/biopet-gatk-extensions/pom.xml
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala 1 addition, 1 deletion...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala 4 additions, 2 deletions...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala 1 addition, 1 deletion.../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala 1 addition, 1 deletion...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala 1 addition, 1 deletion...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala 1 addition, 1 deletion...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala 5 additions, 2 deletions...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala 1 addition, 1 deletion...mc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala 1 addition, 1 deletion...l/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala 1 addition, 1 deletion...biopet/extensions/gatk/broad/RealignerTargetCreator.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala 1 addition, 1 deletion...mc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala 4 additions, 2 deletions.../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
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