Update default options
Remove pipeline_create_commands method
Update resource_class
Add pipeline_wide_parameter method
Update pipeline_analyses
Add options that allow to run only parts of the pipeline when selected
Add species argument
Consider option of only computing consequences for motif_features or
regulatory_features
Add option to not run update vf module
Format code
Add debug option
If debug option is set use only one chrom for running the pipeline
Minor corrections
Adjust analysis array if option only_update_vf is set to 1
Change return value to 0 for in_informative_position if requirements
for computation are not met
Minor changes
Change value in if statement
Add input_ids