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Created with Raphaël 2.2.012Nov11109876543231Oct30292827262523222120191615141312987652130Sep29282725242322211817161413111098765432131Aug302928272625Merge branch 'fix-docs' into 'develop' Fix docsMerge branch 'fix-scaladocs' into 'develop' Fixed scala docs in docsMerge branch 'feature-docs-developers-0.5.0' into 'develop' Change mkdocs.yml to point to the scala docs (only works on server)Update release notes and fix gears titlechange "java -jar command" to biopetFix some explaination about the output directories in the configAdd a bit more on the developer-docs on pipeliningMerge branch 'feature-docs-0.5.0' into 'develop' does changed in doTypoRemoved TODOremove temp from docsadded changes after notes from @a.h.b.bollenMerge branch 'fix-depedencies' into 'develop' Added to the release notesAdd fixmeAdded more to the release notesMerge branch 'fix_gsnap_piping' into 'develop' Disabled intermediate markduplicatesMoved release notes to new folderunify biopet invocation command from java -jar <biopet.jar> to `biopet`Adding mock gearsUpdate some contentMerge branch 'fix-star_version' into 'develop' Added version command for starMerge remote-tracking branch 'remotes/origin/develop' into fix-depedenciesMerge branch 'fix-gentrap_null_pointer' into 'develop' ReformatAdded some scaladocsAdded automated input file checkingfixed jobOutputFileAdded loggingFixed unit testingFixed small bugCatch nullpointersRemove unused importfix method name