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Created with Raphaël 2.2.010Jun87632131May302927262524232019181715141312111098765432130Apr29282726252221181615141312111087654131Mar302925242321191817Merge branch 'feature-sync_stats_report' into 'develop' Added sync stats to reportStyle fixUpdate documentation accordinglyChange default settings to VALIDATED settings .Merge branch 'feature-hisat2' into 'develop' Raise memoryAdded threads flagAdded docsAdded mapping tests for hisat2Added to generateIndexesAdded hisat2build extensionFixed unit testsFixed file nameUpdated to uncompressed downsample filefix rscriptRaise memoryMerge branch 'feature-queue_3.6' into 'develop' Fix shiva variantcallingFix argumentsFormattingFix 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 method