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Created with Raphaël 2.2.03Jun2131May302927262524232019181715141312111098765432130Apr29282726252221181615141312111087654131Mar302925242321191817161514Put 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' Merge branch 'develop' into fix-bedtools_coverage_sortedsort input bed and fix testcreate genome file only once per fasta indexchange ALL licenses across all files.