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Created with Raphaël 2.2.026Feb24231918171615141312111096543230Jan292827262322212019161514131210986517Dec16119854321Fix 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 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 seqstat