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Created with Raphaël 2.2.06Oct52130Sep29282725242322211817161413111098765432131Aug3029282726252423222120191817161514131211643130Jul282724232221171676321Raised some memoryAlways execute fastqc_qcAdded adapters to summaryChange commandLine to cmdLine according to the new specsMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-gearsAdding files to summary jsonMerge branch 'develop' of git.lumc.nl:biopet/biopet into fix-rename-extentsionsfolderFix typoFixing build issuesMerge branch 'develop' into feature-scoverageMerge branch 'develop' into feature-generate_indexesMerge branch 'feature-pipeable' into 'develop' Fix errornous foldernameAdd extension wrapper for biopet, Allow to skipNames in reporting for concise report containing only counts and taxonID'sRemoved out commented testsMoved doc to scala docsAdded scala docsImproved error handeling on executable checkFix cores on bamOutput optionMerge branch 'fix-bammetrics_summary' into 'develop' Remove useless linesFix single end dependencyFix code style warningsRemoved zcat stepMove input for gzip to stdin to not remove fileFixed graph issueFixed summary files of flexiprepFixed issueAdding krakenreport2json to gears pipelineadd WES version of cnmopsFix for #210Simplified tree managementsetupRetry calls setupretry of pipe functionsFix java memory resourceFixed vmemfixed regexFix depsSwitch to CommandLineResourcesUse combine resources for pipesExtracted resoures to trait, usable on non biopet CommandLineFunctions