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Created with Raphaël 2.2.06Sep5432131Aug3029282726252423222120191817161514131211643130Jul28272423222117167632130Jun292827262524232221191716151098765432129May2827261918141312111097Remove unneeded class. java and non-java jobs now both using def cmdLineSwitch bowtie and gsnap to fixed valuesAdded unit tests for fixed valuesCode style fixAdded scaa docsRemove the need of merging the fixedValues anymoreRemove the need of merging the defaults anymoreAddind fixed values to .log folderMake config map immutable from outside the classInit implementation of fixed valuesChanging to SNAPSHOT version, this is following the maven convention VcfWithVcfTest completionResolved small dependency problemsMore tests for VcfWithVcfTestVcfWithVCf refactorMerge branch 'fix-gentrap_strandspec' into 'develop' Fix 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 comment