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Created with Raphaël 2.2.09Nov31Oct20Sep14131211109131Aug2726252420191615141312111087654331Jul3023151420May13116542130Apr27252422732130Mar2726242321201918161514131298628Feb18171514121110743230Jan29282724232221201918171514136311Dec9325Nov2015141186431Oct30292823161511812Septry 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 getRefFix pulled ref mvMove bed only on non ERCCAdd search for ERCC refCombine inputs for getRefInferRemove collect for getRefInferUse channelAdd extractRefData.py as channelRevert eachTry each refInferFix curl queryAdd refSource to param tableAdd deriva auth to getRefUpdate datahub ref downloadUpdate deriva and python containers in config