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Created with Raphaël 2.2.05Mar432127Feb2624231918171615141312111096543230Jan29282726232221Merge branch 'patch-carp' into 'develop'Move custom RScript wrapper to Gentrap directoryAllow custom extensions to have their exes set-up via configFormatting updatesAdd PDF template writing job to main GentrapUpdate wrapper for PDF template writerUpdate base gentrap test with required config value definedMove PDF templates to another directoryFormatting updatesAdd pdf report generator wrapperAdd PDF report templatesModify pdf_report.py with new base layoutAdd templates for plotting scripts and their wrappersDisable untested expMeasure modesExpose enum-based config values as public attributesFormatting updatesAdd variant calling jobs and expose its output as attribute and in summaryAdd extension for simple RNA variant callingAdd fix_mpileup.py script for VarScanAdd VarScan mpileup2cns wrapperAdd VarScan base wrapperAdd default value to SamtoolsMpileup.disableBaqAdd -s and -d flag to SamtoolsMpileupInitial tabix wrapperAdd GatherBamFiles wrapperFix bug that omits md5sum calculation of Flexiprep filesUse GatherBam for merging per-strand jobsFix versionUse correct conditional for optional strand-specific jobsUse correct flag repetition for SamtoolsViewVersionfix on missing AD fieldFix chromosome statsAdded todoAdd strand-specific jobsfix versionfix executableadded bgzip and tabix to freebayesAdded index as input fileAdded tabix