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Created with Raphaël 2.2.08Mar765432127Feb2624231918171615141312111096543230JanUse correct config name for Md5sum override in SummaryQScriptAdd CollectRnaSeqMetrics summary to main Gentrap summaryFix incorrectly parsed CollectRnaSeqMetrics metrics outputAdd chart output of CollectRnaSeqMetrics to summaryRemove aggregated scoverage moduleInitial mapping subsection in reportMerge branch 'develop' into feature-test_coverageMerge branch 'develop' into feature-shivaTweak memory limitFormat scala docsAvoid repeatedly defining the same latex commandFix memlimitUse correct sickle value retrievalAdd all fastqc plots to reportAdding scala docsAdd FastQC parser to PDF report template generatorUpdate report template to output clipped adapter name correctlyUpdate Picard metrics parsing to better handle nonexistent filesAdd fallback job when md5sum job failsAdding scala docsUpdate Sickle wrapper to parse sickle single-end outputAdding scala docsRemove old netbeans filesCatch possible exceptions when parsing table for heatmap plottingUse correct types for JSON output in cutadapt summaryInitial reportFix missing adapter name in flexiprep summaryAdd version to gentrap summary outputFormatting updatesFix sickle wrapper bug causing by incorrect flag outputreleas notes modifications addedreleas notes modifications addedreleas notes modifications addedUpdate test for fragments_per_gene modeFurther trim down testsAdd convenience methods for creating sample configsTrim down general test to test for expMeasure and strandProtocol combinationsAdd more config options to test in GentrapTestFix duplicate value on valid cufflinks measuresRemove addAllJobs from CufflinksProducer