refactor: Update run flags for distance center, process dataset, and qc

[madhavmk]

• Linked to Issue #208
• Make extract-dist-center, extract-process-dataset, and qc CLI arguments default to True

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (4fa0fef) 49.78% compared to head (6a62d90) 49.78%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #210 +/- ## ======================================= Coverage 49.78% 49.78% ======================================= Files 16 16 Lines 932 932 ======================================= Hits 464 464 Misses 468 468 ```

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