TheiaCoV_Fasta_PHB failing when flu_subtype input is blank - Githubissues

theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

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TheiaCoV_Fasta_PHB failing when flu_subtype input is blank #304

Closed jrotieno closed 8 months ago

jrotieno commented 8 months ago

:bug:

:pencil: Describe the Issue

When the flu_subtype input for the TheiaCoV_FASTA_PHB workflow is blank, the workflow calls abricate_flu even for non-flu pathogens.

:repeat: How to Reproduce

Was this run on the Terra platform?
- Terra on GCP or Azure?
Or were the workflows run locally using miniwdl or cromwell?
- 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.

:fishing_pole_and_fish: Expected Behavior

abricate_flu should only be called when the organism input is flu

:floppy_disk: Version Information

:information_source: Additional Information