Refactor `convert_input` to Perform tasks via helper function

[Sweetdevil144]

Description

Following changes were performed :

• [x] Shift functions to check for missing files
• [x] Return from convert_input via a helper function
• [x] Refactor extra variables in run.meta.analysis
• [x] Update corresponding test files and add tests to ensure do_conversions isn't affected by current applied changes

Motivation and Context

The main motive for these changes is to simplify convert_input by trying to break some of its components and branch it to other functions.

This PR may fix a task within #3307

Review Time Estimate

• [ ] Immediately
• [x] Within one week
• [ ] When possible

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• [ ] My change requires a change to the documentation.
• [ ] My name is in the list of CITATION.cff
• [x] I have updated the CHANGELOG.md.
• [ ] I have updated the documentation accordingly.
• [x] I have read the CONTRIBUTING document.
• [x] I have added tests to cover my changes.
• [x] All new and existing tests passed.