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Created with Raphaël 2.2.015May141312111098765432130Apr29282726252221181615141312111087654131Mar3029252423211918171615141311109875432Remove old commentswitch to traitAdded basic testingRename fileFix testFixed testsAdded amplicon testAdded amplicon testAdded test for referenceVcfMove WriteConfig to classAdded dbsnp to configAdded config for each genomeMerge remote-tracking branch 'origin/feature-index_generation' into feature-index_generationFixed testImproved messageAdding tests on normalize stepChanges arg parser with getOrElse(throw new IllegalArgumentException)Added a precheck when using bedfiles with wrong contig in thereAdded check on unused config valuesFixed fifo job namesMerge branch 'fix-toucan_sampleinfo' into 'develop' StyleTest output file neededAdded java matchExtended tests.The files to test on..Extended tests.Fix merge fasta jobFixed code warningsFix improper list type check in ToucanRemove unused importsAdded unit testingFixed fastqcMerge remote-tracking branch 'remotes/origin/develop' into biopet-biosAccept multiple input filesMoved packageMerge branch 'feature-cnvpipeline' into 'develop' Merge branch 'feature-allow-custom-adapters' into 'develop' StyleAccept multiple input files