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Created with Raphaël 2.2.011Dec10764330Nov29272625242320191817161211109876543231Oct30292827262523222120191615141312987652130Sep2928272524232221181716141311109Merge branch 'shiva-refactor' into 'develop' Remove unused importFixed typoStore adapter stats name in a single variableUse correct copyright header for Cutadapt wrapper in Flexiprepfixed importfixed flexiprep summaryAdded reportFixed argsfixed outputDir flexiprepFixed code warningsAdded multisample gears reportFixed unit testingstyle changesAdded SplitLibrariesFastqAdded a defaultUse file names for logging errors in Flexiprep Cutadapt wrapper instead of read namesUpdate None pattern match to use catch-all clauseUpdate adapters summary stats to be Map[String, Any] instead of (String, Int)Initial fix for #238Added flexiprepRemove unused importsFixed argsFixed name output dirFixed args for pickRepSetFixed RepSetFixed argFixed messageStyle fixChanges defaultsFixed argsAdded AssignTaxonomy stepAdded gears to executableChange defaultAdded PickRepSetAdded pickOtus stepAdd empty Qiime pipelineConvert gears to subscriptsCreate sub script for extract unmappen readsCreate sub script for kraken