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Created with Raphaël 2.2.016Mar1210987124Feb232221161413103130Jan292726252422201826Sep2322212019181511830Aug29247Jun63127May2524231713111095226Apr222019181514121198654130Mar28242322211817161514131110987432129Feb262524232222JanAdded peak_type to peak_call markers in generator.Updated peak calling yaml to reflect peak_type.Split spp into narrow / broad peak calls.Updated wrapper parsing and added better wrapper name to spp.Split macs2 into narrow / broad peak calls.Updated create_run to include permutations for peak_type.Added peak types for validation, updated run to validated based on info in configuration.Merge branch '17-idr' into 'master' Finally got idr working due to some issues with python2/python3.Updated strictness of find_result method in run class. If an additional prefix was set on a final result verify it exists in a prev result.Fixed import in download generator.Removed print statements.Fixed issues with saving result. Multiple results can now be successfully marked for saving / loading.Added more memory to idr.Added some helper functions to db / result.Added docstring to find_result.Added idr generator loading to workflow.Added generators to packages list for setup.pyMoved all generators into new folder. Created idr generator. Heavily updated module_generator to support having multiple final_result files.Added the idr module, wrapper, and job files.Added helper functions to result / run for modifying the prefix / metadata and correctly finding results from a run based off a final result metadata.Added support for list arguments.Changed || to or...Updated yaml files to mark final_output. Final output implies both transfer=true and should_save=trueAdded a helper function to find all final_results from workflow_module.Added transfer=true to sorted peak results. Added transfer=false to module_generator download results.Added transfer option to output files to control whether or not it gets transferred.Made the any file extension better.Merge branch '22-gem-output-files-bug' into 'master' Fixed the sort script to include the correct -k1,1V... arguments.Added name to workflow job error print message.Get name_template from peak_call.yaml updates.Updated gem peak calling to list & sort both results. Updated peak_call generator to correctly get ouput file from gem.Added a name_template option for results. This will enable the functionality to override the default name calculation. Since we have access to all jobs being run there is potentital to interpolate arguments. For now we just interpolate prefix where specified.Fixed an issue caused by replace all. ENCODE metadata uses 'experiment_id' not 'experiment_accession'. Also changed name of experiment_inputs to signal_inputs.Renamed cp_bed_tagalign to cp.Merge branch '19-update-database-saving' into 'master' Cleaned up and added documentation for database functions.Merge branch '21-parse-ccat-peakranger-output-into-bed-files' into 'master' Added rewrite option to pass to module_generators. Updated module generators to allow module yaml to specify db saving & prefix type.