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Created with Raphaël 2.2.027Feb2624231918171615141312111096543230Jan292827262322212019161514131210986517Dec1611985432Omit RnaSeqMetrics chart from output summary since it may not existFix output bam files of mappingUpdated ExecutableMerge branch 'develop' into feature-shivaUpdate CollectRnaSeqMetrics wrapper into a SummarizableAdded allele modesAdding UnifiedGenotyperUse correct types for sampleId and libId in GentrapMerge branch 'develop' into feature-gentrapAdd gatk variantcalling with haplotypecallerRemove default value for strandedness protocol in GentrapAdd job for RNA-seq metrics in GentrapAdd validation check to CollectRnaSeqMetrics wrapper on strand specificity flag valueUse correct and explicit types in CollectRnaSeqMetrics wrapperUse correct CollectRnaSeqMetrics main class in wrapperAdd variantcalling to summaryfix formatAdded name prefixesAdded variantcallingFix multiple bugsfix argsAdd CombineVariantsDisable parallel testsChange memory of IGVtoolschange mfold arg parsing, printed empty list when mfold was not givenUpdate formattingAdd more optionsAdded implicit List[File]General gatkMoved to new packageMerge branch 'patch-summary' into 'develop'Fix add jobs to summaryAdd ShivaVariantcallingAdd automatic sample detectionFix formatAdded IndelRealigner and BaseRecalibrationRemove unused importsAdd ShiveGatkMove Shiva to a traitAdded placeholder for addAll