Update annotate injest qc parquet

[jenna-tomkinson]

Description

In this PR, I have updated the external_metadata parameter in annotate to input parquet files and add qc.parquet columns to the profiles prior to the cp_clean helper function to avoid issues with column naming. I also added Metadata_Site as apart of the cp_clean helper function as it is hardcoded for only plate and well so I previously had to make a band-aid for this for projects.

What is the nature of your change?

• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

Checklist

Please ensure that all boxes are checked before indicating that a pull request is ready for review.

• I have read the CONTRIBUTING.md guidelines.
• My code follows the style guidelines of this project.
• I have performed a self-review of my own code.
• I have commented my code, particularly in hard-to-understand areas.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• New and existing unit tests pass locally with my changes.
• I have added tests that prove my fix is effective or that my feature works.
• I have deleted all non-relevant text in this pull request template.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.72%. Comparing base (b93070a) to head (54885d5).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #657      +/-   ##
==========================================
+ Coverage   93.66%   93.72%   +0.06%     
==========================================
  Files          61       61              
  Lines        3992     4018      +26     
==========================================
+ Hits         3739     3766      +27     
+ Misses        253      252       -1     

Flag	Coverage Δ
unittests	93.72% <100.00%> (+0.06%)	⬆️

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