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Created with Raphaël 2.2.010Nov931Oct20Sep14131211109131Aug2726252420191615141312111087654331Jul3023151420May13116542130Apr27252422732130Mar2726242321201918161514131298628Feb18171514121110743230Jan29282724232221201918171514136311Dec9325Nov2015141186431Oct30292823161511812SepTest software version/references multiqc custom report orderingMerge branch 'develop' into '60-consistency_tests'Merge branch '63-on_error' into 'develop'Fix parsing of json file.Fix consistency check for where it is grabbing.Update README.mdTry to fix order.Update DAG, links and order of sections.Add in yaml files.Fix regex markdups.Fix regex.Change patterns and changelong.Bypass markdups exit status of 1.Remove markdups version to see why it fails.try version again.try version again.Update Markdups.Fix output for vrsion of nextflow pipeline.Fix output file for versions.Move to the end.remove jar version.remove seqtk and update output for stdout.Fix test stage name.Add in software versions and references.Updaated documents and changelog and usage statement.Add changelong.fix typo in name of pipeline.Update config for email.Test failure.Update consistency checks to be fully in python.Reduce species inference cutoffs0.0.4_indev0.0.4_indevMerge branch '23-ref.to.datahub' into 'develop'Update docs/dag.pngFix elifFix datahub specific bed folder moveAuto pep8'd all python codeUpdate changelogFix ref move after getRef datahub pullUpdate docsAdd refName to getRef