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Created with Raphaël 2.2.026Jan252019181514121110987654330Dec292827171475230Nov20191413121110931Oct20Sep14131211109131Aug272625242019161514131211108765Fix new force var namesRemove unnecessary excapeAdd missing excapesFix qutes to echoAdd qutes to echoAdd force params for stranded and spikeDouble excape slashExcape bash varsUpdate create test data with new metadata modelUpdate create test data with new metadata modelURLify hatrac location for outputBagFix getRef use of new spike valuesUpdate parseMetadata ci testTemporarily change CI integration tests to use dev server (staging doesn't have model changes)Change logic for uploadOutputBagMerge data error pre-Execution runAdd blank mRNA_QC on data failRemove unnecessary RID output parsingConvert strandedness from yes/no to t/fConvert strandedness from yes/no to t/fUpdate Has_Strand_Specific_Information to StrandednessUpdate Sequencing_Type to Experiment_TypeAllow Single Read for backwards compatibilityFix Single Read in CIUpdate changelogChange Single Read to Single EndMerge branch 'develop' into 'master'Update errors in readmeMerge branch '108-samtools.mem' into 'develop'Update DAGUse 1 less process for samtools threading and limit memto 75% of availableMake sampled align use > 32GB nodes on BioHPCCatch error if fastq file error grepFix fastqc error detectionAdd back ends manual to parse ci unitAdd back ends manual to ci unit for parse, but manualAdd unexpected meta and fastq structure error ci integration testsAdd excape to bracket in echoRemove ends manual from parse metadata unit ciAdd premature fail execution run upload with fastq file error