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Created with Raphaël 2.2.02Feb129Jan28272625232221201918171514121110865430Dec29282625242322211817161514131110764330Nov29272625242320191817161211109876543231Oct3029282726252322Report update, sorting order (display)Adding regex for the Cutadapt 1.7+Fixed bug in LnAdded md5 check to pipelineMerge remote-tracking branch 'remotes/origin/develop' into feature-qiimeAdding additional GTF annotation for the other smallRNAfixed default name for output fileRemove outputDir as output filefixed output file of basecounterFixed summary jobstoucan docsAdded test on main methodAdded more testingRemove bed annotationAdded testing on Count classesAdded basic testsTesting with trimming all sequences - in flexiprepLimit reporting of events in REF/ALT col to < SVTYPE > (saves space and post-processingpower)Fixed bammetrics testsAdding samplingSize to BamUtils - estimateInsertSizewgs and rna metrics now got config value to enable/disable themFixed units testsOutput strandspecific wiggle/bigwig and TDF filelowering the minimum_length to be keptswitch to core rscript extensionAdded insert size estimation. Fix pindel2vcf dependency (depend on pindel, use beforegraph to set outputpath)fix code warningsAdded meta exon counts to pipelineFixed scopeMerge remote-tracking branch 'remotes/origin/develop' into feature-measure_modulesRemove old unused codeReformatAdded meta exons countsFixed gentrap testschange typo in gentrap docInsertsize estimatoradded fastq extension disclaimer to pipeline docsreorder levelsFix code warningsFixed createMetaExonCounts method