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Created with Raphaël 2.2.03Jun2131May302927262524232019181715141312111098765432130Apr29282726252221181615141312111087654131Mar3029252423211918171615FormattingFix outputpath for the individual contig outptuUpdate on the CNmops wrappers and Kopisu pipeline (call for all contigs in the genome)Add documentation for hisat2 support in gentrapPut scattering back in for baserecalibrationSwitch to Queue 3.6Add hisat2 to mappingEnsure the correct hisat2 index extension is detectedStyle updatesAdd initial hisat2 wrapperMerge branch 'fix-bedtools_coverage_sorted' into 'develop' Merge branch 'feature-imptute_to_vcf' into 'develop' Merge branch 'fix-haplotypercaller' into 'develop' autostyle fixesAdding CNmops as method to KopisuChange val nameSwitch to picard for id sortingdownsampling after QC step of gearsMerge branch 'fix-star-mapping-keep-unmapped' into 'develop' remove gvf methodfixed a config valueFix lowercaseSet default star to output unmapped reads also in the bamfileFixed testsStyle fixesMerge remote-tracking branch 'origin/develop' into developAdded down sample option after stichingFixed adapter feedingStyle changesChanged custom adapters feedingMerge branch 'fix-mapping_precentage' into 'develop' Merge branch 'feature-autodetect_paired' into 'develop' Added downsample option to gearsAdding seqtk sample extensionInit commit for bamstatsMerge branch 'feature-unique_sample_filter' into 'develop' Added autodetect fileformat pairedAdding error on missing allelesExtract impute to vcf as separated pipelineMerge branch 'fix-gatk-license' into 'develop'