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Created with Raphaël 2.2.09Mar8765432127Feb2624231918171615141312111096543Update Tabix wrapperConfig name changeFormatting updatesUse correct threads and mem values for Cufflinks and Gsnap wrapperFix bug in JAR run caused by copying entire resource folderMerge branch 'feature-scaladocs' into 'develop'Update Cufflinks defaults for cluster runUpdate GSNAP defaults for cluster runUpdate report templateAdd sample-level bam metricsMake sample-level metrics optional, instead of library-level metrics (for RNA)Add library pair information to sample metricsAdd library-level and sample-level RNA metrics to reportAdd per-library RNA metrics job when the sample contains more than 1 libraryUse MergeSamFiles for all mergesDefault to not using MarkDuplicates PG tag as it creates conflicts when merging BAM filesUse correct alignment file for per-sample CollectRnaSeqMetrics jobUse 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 files