fix: cleaner data handling and improved logic for sample_qc_table.py (issue #324)

[jaamarks]

This PR builds upon the changes introduced in PR #327 to further refine the sample_qc_table.py script and address issues related to sample retention.

What

• Refactor: Removed the use of "Sample_ID" as the index in _retain_valid_discordant_replicates function.
• Data Type Fixes: Resolved various datatype issues throughout the code.
• Function Order Change: Reordered the _add_identifiler function to follow the _add_analytic_exclusion function.
• Column Update: Replaced "is_cr2_filtered" column to the "is_call_rate_filtered" column in the _retain_valid_discordant_replicates function.
• Test Updates: Updated the corresponding tests in tests/workflow/scripts/test_sample_qc_table.py. Added the "is_call_rate_filtered" column to the fake_sample_qc data fixture.

Why

• Issues arose from using "Sample_ID" as the index in _retain_valid_discordant_replicates. Refactoring the code to eliminate this dependency resolves those issues.
• Bugs related to datatypes were fixed by converting the variables to the correct data types.
• Reordering the _add_identifiler function to follow the _add_analytic_exclusion function allows the _retain_valid_discordant_replicates function to run first, accommodating any status changes to "is_discordant_replicates".
• Using the "is_call_rate_filtered" column instead of the "is_cr2_filtered" provides clearer indication of whether a sample failed either call rate filter.
• Since we are now referencing the "is_call_rate_filtered" column in the _retain_valid_discordant_replicates function, we aligned our test data with this new expectation.

Fixes #324