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Created with Raphaël 2.2.013Nov121110931Oct20Sep14131211109131Aug2726252420191615141312111087654331Jul3023151420May13116542130Apr27252422732130Mar2726242321201918161514131298628Feb18171514121110743230Jan29282724232221201918171514136311Dec9325Nov2015141186431Oct30292823161511812SepUpdate changes to reflect only the change in order of steps. Fix output files.Fix extra space.Remove pigz parllel option.Update with set for since only 1 variable. Also update pattern to pass files.Add back parallel trim step. Moved fastqc step after trim.Update bicf_logo.pngMerge branch '78-tool_version' into developMerge branch '60-consistency_tests' into 'develop'Fix id in generate versions.Fix number of reads that map. Merge branch '78-tool_version' of git.biohpc.swmed.edu:gudmap_rbk/rna-seq into 78-tool_versionAddress typo's and refernces to pipeline.Fix custom report names for orderingTry to get software references workingFix spelling errorTest 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.