Resolve "IDR"

Closes #17 & #23

See merge request !21

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 issues with saving result.  Multiple results can now be successfully marked for saving / loading.

Moved all generators into new folder.  Created idr generator.  Heavily updated module_generator to support having multiple final_result 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.

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

Added transfer=true to sorted peak results.  Added transfer=false to module_generator download results.

Resolve "Gem output files bug"

Closes #22

See merge request !20

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.

Cleaned up and added documentation for database functions.

Closes #19

See merge request !19

Resolve "Parse ccat / peakranger output into bed files"

Closes #21, #20 

Fixed several workflow bugs -- everything is functioning pretty normally now!  Results are getting loaded and saved correctly.

See merge request !18

Added rewrite option to pass to module_generators.  Updated module generators to allow module yaml to specify db saving & prefix type.

Added correct commands for parsing jobs.  Fixed naming conventions for ccat, and updated the prefix.