TheiaCoV_ONT: prevent failure by coercing files into strings

[sage-wright]

Closes #270

:hammer_and_wrench: Changes Being Made

To prevent workflow failure when read screening fails, this PR coerces the File assembly_fasta output into a String. Outputs behave the same on Terra, but workflow failure no longer will occur.

Also, some redundant ? were removed

Impacted Workflows/Tasks

• TheiaCoV_ONT

:brain: Context and Rationale

"" cannot be evaluated as a File, but a File can be evaluated as a String.

:clipboard: Workflow/Task Steps

No change

Inputs

No change

Outputs

No new outputs

Impacted Outputs

String assembly_fasta

:test_tube: Testing

Locally

Terra

No original failures (before change) in read screen: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/17bbd163-1949-431f-a745-b4d5c9d15193

Original failures (before change) in read screen: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/4443d283-9729-42f8-ae4b-596a13c1800d

Scenarios for Reviewer to Test

• Samples that fail the read screen
• Samples that pass the read screen

:microscope: Quality checks

Pull Request (PR) checklist:

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