Update typingQC to align with mikrokondo and CDC

[kylacochrane]

Summary

Updates to three typingQC pipeline modules to support a new mikrokondo QA field, fix a pre-existing schema mismatch, and add serovar nomenclature handling.

sequenceQC.py

• Added wgmlst_loci_count to QA handling: captured as a warning test but returns PNC_FAIL_MESSAGE on failure
• Fixed CHECKM_TEST constant: checkm_contamination → checkm2_contamination to match current mikrokondo JSON schema

sistrQC.py

• Strip non-actionable INFO: Number of cgMLST loci found message from qc_messages before reporting
• Wzx/Wzy-only FAIL samples no longer block typingQC: serovar reportability is still checked and quality_metrics reports a warning instead of a raw FAIL message

validateSerotype.py

• Added CDC serovar rename mappings: Panama → Panama/Houston, Sendai → Miami
• Sendai renames append a nomenclature warning to quality_metrics
• Rename logic is table-driven for easy extension

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

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Hi @kylacochrane,

It looks like this pull-request is has been made against the phac-nml/typingQC main branch.
The main branch on phac-nml repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the phac-nml/typingQC dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!