GitLab

Fixed a validation error with jobs with non-required arguments.  Trying to evaluate numeric types without a value.

Updated file interpolation to use literal name instead of object.  This will make some edge case parsing easier in the future.

Updated 3 things: 1st changed pepr arguments to be a list with a separator.  Updated argument parsing to allow joining list arguments with another value.  Updated conf to allow separator as a valid argument option.

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.

Updated param files and remove_duplicates yaml & generator to successfully generator job.  Fixed a bug where workflow_job validation was crashing on non-string values.

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_job to use internal type values for arguments instead of passed ones.  No longer need types included in workflow_module.

Removed unnecessary print statement.  Added optionally argument loading.  Fixed valid workflow generation test.

Job argumnet creation is now actually legible AND works with the new style of inputs/outputs as well as job definition files.

Heavily updated workflow_job parsing & validation.  Addeded several tests to confirm the validity of new parsing.  additional_inputs no longer exist, and input / output files are defined as dicts instead of lists.  References refer directly to the dict key names instead of a list index.

Added initial sphinx doc tree & build stuff.  Using the sphinx markdown theme.  Use 'make html' to build the docs.

Updated validation, error parsing, and param parsing.  Params specific to the job are now expected to be passed by the workflow.  file list arguments MUST have file_type defined.