Feature request: Remove Hardcoded Values and Move to Configs

[berntpopp]

Remove Hardcoded Values and Move to Configs

Description:
Remove hardcoded values, including conda environments and reference files, from the scripts and move these configurations to the config files. This will enhance the flexibility and reusability of the scripts.

Acceptance Criteria:

• Remove hardcoded conda environments and reference file paths from the scripts.
• Update the config files to include these values.
• Ensure the scripts read these values from the config files.
• Update the documentation to reflect these changes.

Implementation Steps:

1. Identify hardcoded values in the scripts.
2. Move these values to the config files.
3. Update the scripts to read the values from the config files.
4. Test the updated scripts to ensure they work with the new config settings.
5. Update the documentation with the new configuration instructions.