Small updates to many yaml files.  All peak callers now generating successfully.  Adjusted file_list input loding.  Fixed chip-job-ccat-format-bed to create correct number of columns.

Adjust the input format of the align.yaml module.  Fixed up minor issues across workflow job, module, and generator to get jobs correctly generating.

Updated workflow module parsing to support new format.  Argument types are now loaded from workflow_job data instead of being repeated within the module itself.

Moved the constructor auto-doc to the correct place.  Added auto-doc for missing functions, and removed unused methods.

Updated yaml files to mark final_output.  Final output implies both transfer=true and should_save=true

Added 'list' argument to allow vararg inputs. Updated workflow_module & job accordingly to handle new input type.

Added debug variable to workflow_module.  Fixed intra module file dependency issues, by passing output files to setup_job_params.

Removed all instances of prefix in workflow_module.  Fixed setup_job_params to correctly index files from the master_files list.

Refactored module_workflow code.  Module creation now requires inputs, additional_inputs, and outputs.  Updated parameter validation and interaction with the dax.  Add documentation to all functions.

Updated all yaml files to support type argument.  Heavily updated workflow_job parsing and verbosity.

Create save_result function in workflow.  Updated workflow_job & module to provide additional necessary info to save database results.

Added db_save_results yaml job, and script.  Updated workflow information tracking to create correct meta data files for saving information to the database.  Conf adjusted to support yaml files, and arbitrary result files.  workflow_job can now return a dictionary of all arguments used.

Fixed param files to reference correct commands.  Updated workflow job loading to use commands specified within yaml files.  Added a debug mode to workflow to print out additional statements.

Fixed issues with submitting multiple jobs for same files.  Added new example to find experiment_ids from the T4 and HM collections. Download now prioritizes hcc_url if it exists.

Updated stdout & stderr redirection.  Includes adjustments in individual job yaml files, module yaml files, and workflow generation handling.

Fixed reference to undefined variable key in workflow_module.  Adjusted param files to use bed arguments

Fixed typo in remove_duplicates.yaml.  Adjusted get_full_name to handle no markers.  Updated workflow to track prefixes cross module.