This PR addresses an issue found during validation where the type for the krakrn2 report output was not being passed correctly to the export taxon table task.
This has been patched.
Impacted Workflows/Tasks
TheiaProk suite of workflows:
TheiaProk_Illumina_PE
TheiaProk_Illumina_SE
:brain: Context and Rationale
export taxon tables task was expecting a File input for the kraken_report but due to it being an optional output, it is being handled as a String by the Theiaprok workflow (SE and PE).
Closes #298
:hammer_and_wrench: Changes Being Made
This PR addresses an issue found during validation where the type for the krakrn2 report output was not being passed correctly to the export taxon table task.
This has been patched.
Impacted Workflows/Tasks
TheiaProk suite of workflows:
:brain: Context and Rationale
export taxon tables task was expecting a
File
input for thekraken_report
but due to it being an optional output, it is being handled as a String by the Theiaprok workflow (SE and PE).:clipboard: Workflow/Task Steps
Inputs
N/A
Outputs
N/A
Impacted Outputs
:test_tube: Testing
Locally
N/A
Terra
Set of 20 bacterial genomes with taxon tables task enabled, as well as kraken2 optional module (one expected failure due to SRA lite file format issue): https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/805a3537-a339-4b05-99bd-8ec4c1b18a32
Scenarios for Reviewer to Test
:microscope: Quality checks
Pull Request (PR) checklist: