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Created with Raphaël 2.2.013Feb12111096543230Jan292827262322212019161514131210986517Dec1611985432128Nov272524222120191817141211108765Make better use of the File object, let the file object concat the paths for meRename and use string formattingFix outputdirsFix output dirsSet default vmem to 5GAdd job check to unit testsremove timestampRemove unused importsAdd wrapper for CuffquantUse correct default value for Cufflinks output directoryIntial unit test for CarpAdded default alignerclean bd2vcf converter a bit..Added test log4j.propertiesUpdate Cufflinks wrapperRefactor HTSeq-count jobs creation and its output accessMerge branch 'feature-bamToBigWig' into 'develop'Convert flexiprep testing to DataProviderAdded star-2pass and stampy to data provider, not having 192 unit testsFix some config valuesAdded 128 unit tests to mapping pipelineFix typosFix "/" format errorsMake reference absoluteMake outputDir always absoluteBreakdancer vcf should output more headers, adding official header for SVsAdded asFileFix typoRemove unneeded "/"Format fixFix error messageMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-cnvpipelineFreeC wrapperChange name checkExecutable to preProcesExecutableRename afterGraph to beforeGraphFix some small bugsAdded flexiprep testingFix RPKM directory path from configChange globalConfig to defFormat fix