Is your feature request related to a problem? Please describe.
The current ShigaPass/FastANI taxonomy reconciliation logic is split between the Nextflow CHECK_SHIGAPASS_TAXA process and check_taxa.py, making the workflow harder to follow and maintain.
In addition, ShigaPass reports Shigella species using abbreviated identifiers such as SS, SF, SB, and SD, while the FastANI taxonomy contains full species names. Therefore, the current Bash species comparison generally treats them as different and passes Shigella samples to check_taxa.py anyway.
Describe the solution you'd like
I propose moving the reconciliation logic into check_taxa.py so that Python becomes the single source of truth for updating the FastANI taxonomy based on the ShigaPass result.
When ShigaPass identifies Shigella, the Shigella species should be updated directly from the ShigaPass result.
Additional context
ShigaPass is only run for samples classified by FastANI as Escherichia or Shigella, so the reconciliation can be handled entirely within check_taxa.py.
Is your feature request related to a problem? Please describe.
The current ShigaPass/FastANI taxonomy reconciliation logic is split between the Nextflow
CHECK_SHIGAPASS_TAXAprocess andcheck_taxa.py, making the workflow harder to follow and maintain.In addition, ShigaPass reports Shigella species using abbreviated identifiers such as SS, SF, SB, and SD, while the FastANI taxonomy contains full species names. Therefore, the current Bash species comparison generally treats them as different and passes Shigella samples to
check_taxa.pyanyway.Describe the solution you'd like
I propose moving the reconciliation logic into
check_taxa.pyso that Python becomes the single source of truth for updating the FastANI taxonomy based on the ShigaPass result.When ShigaPass identifies Shigella, the Shigella species should be updated directly from the ShigaPass result.
Additional context
ShigaPass is only run for samples classified by FastANI as Escherichia or Shigella, so the reconciliation can be handled entirely within
check_taxa.py.