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Created with Raphaël 2.2.014Jul20May13116542130Apr27252422732130Mar2726242321201918161514131298628Feb18171514121110743230Jan29282724232221201918171514136311Dec9325Nov2015141186431Oct30292823161511812SepAdd pipeline version var to trackUpdate nextflow and singularity versions in CIFix param reference in runtime infoAdd runtime infoAdd unsorted deduped bam to test_data creationFix new CI unit testsAdd script to create test dataUpdate CI unit tests to use repRID Q-Y5F6Add unit test run for all mea parseta parsedFix 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'