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Created with Raphaël 2.2.020May13116542130Apr27252422732130Mar2726242321201918161514131298628Feb18171514121110743230Jan29282724232221201918171514136311Dec9325Nov2015141186431Oct30292823161511812SepFix cp error for fastq names with multiple R1/2Stage experiment settings as ExperimentSettings.csv to prevent bash errorAdd source param for getBag #50Fix fastq output name fixFix fastq output nameGeneralize destination filename for fastq qxtractionGeneralize find fastq after fetchChange to staging.gudmap.orgChange fetched fastq's mv to cv... mv was truncating some filesFix getDataFix multiqc outputHarmonize outputs, add multiqc outputHarmonize logsHarmonize process logs (remove excess)Harmonize process commentsHarmonize in script commentsFix featureCountsFix stranded inference logicFix floating point errorsFix SE alignSampleSummary output nameFix SE downsample output optionalFix report orderAdd experiment and study rid's to multiqc reportAdd metadata and repRID to multiqc reportMerge branch 'develop' into '10-process.aggregateQC'Add all reports(except metadata)Fix next line in trackStartFix repRID in trackStartAdd quotes to repRID in trackStartFix trackStartMerge branch 'develop' into '10-process.aggregateQC'Merge branch 'track.pipeline' into 'develop'Add extra params for trackingMerge branch 'track.pipeline' into 'develop'Add ci flag from trackingChange pipeline tracking to curlAdd trackStartAdd more columnsMerge branch '47-move.inference' into 'develop'Resove merge comments from @venkat.malladi