refactor: simplify ShigaPass/FastANI taxonomy reconciliation logic

[weichisyu]

Simplify ShigaPass taxonomy reconciliation ( issue #223)

This PR moves the ShigaPass/FastANI taxonomy reconciliation logic into check_taxa.py instead of splitting the decision-making between the Nextflow process and Python script.

Changes

1. Move ShigaPass/FastANI taxonomy reconciliation logic into check_taxa.py
2. Interpret ShigaPass results as either:

• Shigella
• Escherichia when the result is EIEC or Not Shigella/EIEC

3. Convert FastANI Escherichia calls to Shigella when ShigaPass identifies a Shigella type.
4. Convert FastANI Shigella calls to Escherichia coli when ShigaPass reports EIEC or Not Shigella/EIEC.
5. Always update the Shigella species from the ShigaPass result when ShigaPass identifies Shigella.
6. Validate that the incoming FastANI genus is either Escherichia or Shigella
7. Preserve the original formatted ANI output when no taxonomy update is required.

Why update all Shigella species?

ShigaPass reports Shigella species using abbreviated identifiers such as SS, SF, SB, and SD, whereas the FastANI taxonomy contains full species names.
The previous Bash comparison therefore generally treats the ShigaPass and FastANI species values as different and passes the sample to check_taxa.py anyway.
Instead of keeping this redundant comparison in Nextflow, this PR sends the reconciliation decision directly to Python.
When ShigaPass identifies a sample as Shigella, the ShigaPass species assignment is used to update the taxonomy.

Resulting logic

ShigaPass classification	FastANI classification	Action
Shigella	Escherichia	Convert to Shigella and update species
Shigella	Shigella	Update species
EIEC ; Not Shigella/EIEC	Shigella	Convert to E. coli
EIEC ; Not Shigella/EIEC	Escherichia	No taxonomy change

This keeps the reconciliation logic in one place and makes the intended relationship between FastANI and ShigaPass easier to understand and maintain.