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Created with Raphaël 2.2.09Mar8765432127Feb2624231918171615141312111096543RCommandlineFunction TraitRCommandlineFunction TraitAdd Tophat to Mapping moduleAdd functional Tophat wrapperMerge branch 'patch-mapping' into 'develop'Fix error on zipped input without flexiprepAdd initial version table to reportForce version retrieval and path resolution in CustomVarscanMerge branch 'develop' into feature-gentrapMerge branches 'develop' and 'docs_v.0.3.0' of git.lumc.nl:biopet/biopet into docs_v.0.3.0Merge branch 'patch-summary_versions' into 'develop'Merge branch 'patch-seqstat' into 'develop'More efficient codeMore efficient case classFix array out of bound errorFix 'n' bug for seqstatFix Some(versions)Merge branch 'develop' into feature-gentrapAdded notesUpdate 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 summary