virulencefinder is not triggered for Shigella sonnei

:bug:

:pencil: Describe the Issue

It seems that due to the way that merlin_tag's are assigned by GAMBIT and the way that the taxon-specific tasks are configured in the merlin_magic subworkflow, samples identified as Shigella sonnei (gambit_predicted_taxon output) are not run through virulence finder.

:repeat: How to Reproduce

Was this run on the Terra platform?
- Terra on GCP or Azure? Terra on GCP
Or were the workflows run locally using miniwdl or cromwell? No
- What was the exact command was used to launch the workflow?
If possible, we may ask you to share your Terra workspace with us. Usually READER access is sufficient, but we may ask for WRITER access if we need to make changes to the workspace to reproduce the issue.

Run a Shigella sonnei sample through a TheiaProk workflow v1.2.1 (likely Illumina PE workflow)

:fishing_pole_and_fish: Expected Behavior

Expect virulencefinder to be run on all Escherichia and Shigella species.

:floppy_disk: Version Information

All, but tested with v1.2.1

:information_source: Additional Information

I think we need to be very careful about making these adjustments and ensure that merlin_tag's are set in the GAMBIT task properly & that the merlin_magic subworkflow is updated to allow for Shigella sonnei to also be run through virulencefinder

There are some other similar bugs like this that need to be addressed. Would be good to open these as separate issues & PRs unless we can do one big sweeping PR that fixes many of these issues.

theiagen / public_health_bioinformatics