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Created with Raphaël 2.2.03Sep2131Aug3029282726252423222120191817161514131211643130Jul28272423222117167632130Jun292827262524232221191716151098765432129May28272619181413121110974130Apr2928Fix strand-specific separation in GentrapMake FreeC work with only bam filesWriting the config file now waits till pipeline is finishedMerge remote-tracking branch 'origin/develop' into feature-cnvpipelineMerge branch 'fix-scalariform' into 'develop' Merge remote-tracking branch 'origin/develop' into feature-cnvpipelineAdded an importMove generate indexes to own maven artifactMerge branch 'fix-vepnormalizer' into 'develop' Scalariform needs a non empty src dirSome extras for VcfWithVcfTestMerge branch 'feature-option_keep_files_flexiprep' into 'develop' Fix for #198Merge branch 'fix-chunk_metrics' into 'develop' SummaryToTsvTestRefactoring SummaryToTsv to make it more testableMerge branch 'martijnvermaat-readme-fixes' into 'develop' Remove template from frameworkAdded MultisamplePipelineAdded Some more todo'sAdded example of a biopet executableAdd todo'sAdded a simple pipeline as exampleAdded a commentFix nameSwitch to only 1 maven artifact as exampleAdded single pipeline exampleChange queue version in docsFixed linksMerge branch 'readme-fixes' of git://github.com/martijnvermaat/biopet into martijnvermaat-readme-fixesReplace getCanonicalPath for getAbsolutePathNo chunk_metrics when chunking is disabledAdding some todos to seq statNow it does only the files of 1 modulegetorelsedocfix for #196Fix most of #196. Only documentation remainingPartial #196. Split up in functions.Should not forget to add the resourcesTests for SamplesTsvToJsonTest. Some of these will fail before #196 is resolved.