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Created with Raphaël 2.2.023Nov20191817161211109876543231Oct30292827262523222120191615141312987652130Sep29282725242322211817161413111098765432131Aug302928Fixed nameprefixAdded tbi output fileAdded module to config valueAdding decompose option to shivaAdding vt decompose extensionAdded normalize option to shivaFixed argsAdded vt normalizer extensionFixed summary jobs for carpAdded vcf stats for each region bed fileRemove addSummaryJobs()Split variantcalllers in separated filesFixed bowtie indexMerge branch 'develop' into feature-vardaCRLF issue fixedMake compilable version after merging in changes from DevelopBumb version to 0.5.0-RC1Fixed license headersMerge remote-tracking branch 'origin/feature-cnvpipeline' into feature-cnvpipelineSync with developFixed License filesSync with developMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-delly-mergeMerge branch 'fix-tools_mainclass' into 'develop' Fixed bug in loading the mainClass for biopet toolsMerge branch 'feature-docs-0.5_quickfix' into 'develop' Merge branch 'feature-core_testing' into 'develop' rewrite of varda implementation. It now must take a normal call VCF, *and* a GVCF.Merge branch 'fix-toucan' into 'develop' Error in Gentrap sample config in DocumentationAdded tests for resourcesStyle changesAdded test on pipeline nameChange some value to non-freevarChanged loggingAdded test to SampleLibraryTagAdded unit testsMake sure toucan creates bed track for varda based on all calls (including ref calls!), but only upload variants in vcf.Merge branch 'fix-gentrap_samples_dir' into 'develop' Remove override method, now uses the bases class