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Created with Raphaël 2.2.019Oct1615141312987652130Sep29282725242322211817161413111098765432131Aug3029282726252423222120191817161514131211643130Jul2827added dependency for combinevariantsMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-gearsStyle update by IDEAUpdated krakentojson report and enforce check-names with-in KrakenUse provided exts Set instead of zipExtensionsRemove R1_ext and R2_ext from FlexiprepHandle RNA seq files, sam filter only takes the primary alignmentAdd error message when a Flexiprep input file does not have the expected structureRefactor filename and extension retrieval in Flexiprepadd bcf merge to shiva and create wrapperMerge branch 'fix-memory_test_threads' into 'develop' Limit memory for each test threadStyle fixMerge branch 'feature-parralel_mapping_tests' into 'develop' added tabix to bcftools outputfix shiva testMerge branch 'develop' into feature-cnvpipelineMerge branch 'develop' into feature-generate_indexesMerge branch 'feature-dev_docs' into feature-docs-0.5.0Merge branch 'develop' into feature-docs-0.5.0Merge remote-tracking branch 'remotes/origin/fix-mapping' into feature-parralel_mapping_testsGentrap test are now divided over 7 threadsRename fileRemove some test and optimize codeEach aligner has his own class nowadded proper piping to bcftools and mpileup. [GENTRAP VARSCAN SHOULD BE TESTED]Merge branch 'feature-scoverage' into 'develop' Added jobs to pipejobsRemove "reference" from testingRemove "reference" from testingCode styleFix code warningsdependency graph is now correctadded bcftools_singlesampleFixed version to single end executablesFix picard versionsOutput singleton reads (in case the input bam had dedup with removal turned on)autofixesget sample names from vcf when pipeline is started by itselfcreate config on the fly