[TheiaProk suite] Patch fix: change type of kraken2_report to be string in taxon_table task

[cimendes]

Closes #298

🛠️ 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:

• TheiaProk_Illumina_PE
• TheiaProk_Illumina_SE

🧠 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).

📋 Workflow/Task Steps

Inputs

N/A

Outputs

N/A

Impacted Outputs

🧪 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

🔬 Quality checks

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The workflow/task has been tested locally and on Terra
• The CI/CD has been adjusted and tests are passing
• Everything follows the style guide

[sage-wright]

will merge once CI is working

[kapsakcj]

CI updated and fixed. thanks for this change.