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Created with Raphaël 2.2.026Feb24231918171615141312111096543230Jan292827262322212019161514131210986517Dec1611985432128NovAdd ShivaVariantcallingAdd automatic sample detectionFix formatAdded IndelRealigner and BaseRecalibrationRemove unused importsAdd ShiveGatkMove Shiva to a traitAdded placeholder for addAllComplete preproces stepsFix argumentAdded shiva to executableFirst commit for ShivaMerge branch 'patch-macs2-callpeaks' into 'develop'Update R script to accept commandline arguments with optparseMerge branch 'patch-summary_md5' into 'develop'Fix to redirect md5 to be write in the ouput dirFix to redirect md5 to be write in the ouput dirMerge branch 'patch-bowtie' into 'develop'Fix importsFix bowtie when doing paired endAdded a commentFix output folders for scoverageFix typochange mfold arg parsingMerge branch 'feature-summary' into 'develop'Remove old seqstatAdded new summary to new seqstatFix missing importMerge branch 'develop' into feature-summaryAdded test code coverage pluginMerge branch 'feature-seqstat-scala' into 'develop'Add RScripts and functional RScriptCommandLineFunctionFixing seqstat usage of outDirMerge branch 'feature-seqstat-scala' into 'develop'Merge from developMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-cnvpipelineRScript commandline function wrapperAdded mroe docsAdde more docsSaver get