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Created with Raphaël 2.2.03Aug19Jul7616Jun15141312986532131May3026242322191817161211874228Apr2521201312529Mar282017161210987124Feb232221161413103130Jan292726252422201826Sep2322212019181511830Aug29247Jun63127May2524231713111095226Apr222019181514121198654130Mar28242322211817161514Merge branch 'sample-genome-assembly-naming' into 'master'mastermasterModify chip-meta-import to first try and set the genome type based on the sample file information instead of the experimentAdd non-zero exit code.Add condition to check if file is empty before uploading it to MongoDBMerge branch '36-chip-meta-download-should-support-resuming' into 'master'Add resume option to meta download script.Updated installation documentation.Added bridges example. Updated chip-gen doc.Added sphinx autodoc for email param.Fixed up a few more minor issues.Removed unnecessary conf argument from chip-gen.Added email argument, removed all references to config file.Removed config files as being necessary. Added chip-bin and idr bin argumens to workflow & chip-gen scripts.Merge branch '26-zerone' into 'master' Should be broad & sharp for pepr.need to include sharp somewhere in peak_call yaml so it gets loaded correctly.Merge branch '26-zerone' of git.unl.edu:hcc/chipathlon into 26-zeroneUpdated pepr yaml files to copy duplicate control / signal files under new name.Replace narrow with sharp peak type for PePrMinor doc fixes.Updated the getting started example to be up-to-date.Added two missing links to tools.Updated all of the scripts. Made a convenient script for writing the scripts documentation...Fixed peak call yaml for pepr.Fixed a validation error with jobs with non-required arguments. Trying to evaluate numeric types without a value.Added disclaimers to formatting jobs.Fixed arguments for pepr peak calling. Updated params in peak_call module to correctly reflect the output files produced by hidden domains.Added more debug statements and fixed file_list parsing in workflow_job.Removed non-existant verbose argument. Removed input/output directory options.Fixed typo in download from gridfs updated localpath to local_path.Fixed lots of minor bugs to make sure the workflow actually generates! Running tests now.Finished resolving merge conflicts. There were a lot.Fixed minor bug with duplicate dependencies being added to the workflow.Merge branch '34-mongodb-auth-should-be-optional' into 'master' docsdocsUpdated gen script to use db info as keyword not positional arguments.Fixed issues with circular dependncy in utils / db.pyFixed merge conflicts again...?Initial master merge into optional mongo branch.Merge branch '35-workflow-job-parsing-update'Merge branch 'bridges-compatability' into 'master'