TheiaValidate: Compare file contents (#264)

[sage-wright]

This PR closes the loop on the adding file comparisons to TheiaValidate

🗑️ This dev branch should be deleted after merging to main.

:brain: Aim, Context and Functionality

This PR pushes the changes into main that have been thoroughly tested as part of #264

:hammer_and_wrench: Impacted Workflows/Tasks & Changes Being Made

This will affect the behavior of the workflow(s) even if users don’t change any workflow inputs relative to the last version : No

Running this workflow on different occasions could result in different results, e.g. due to use of a live database, "latest" docker image, or stochastic data processing : No

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed:

TheiaValidate updated to now compare files

Databases or database versions changed:

Data processing/commands changed:

File processing changed:

Compute resources changed:

➡️ Inputs

⬅️ Outputs

File comparison outputs now created

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Terra Testing

Suggested Scenarios for Reviewer to Test

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

• [x] The workflow/task has been tested locally and results, including file contents, are as anticipated
• [x] The workflow/task has been tested on Terra and results, including file contents, are as anticipated
• [x] The CI/CD has been adjusted and tests are passing (to be completed by Theiagen developer)
• [x] Code changes follow the style guide

🎯 Reviewer Checklist

• [x] All impacted workflows/tasks have been tested on Terra with a different dataset than used for development
• [x] All reviewer-suggested scenarios have been tested and any additional
• [x] All changed results have been confirmed to be accurate
• [x] All workflows/tasks impacted by change/s have been tested using a standard validation dataset to ensure no unintended change of functionality
• [x] All code adheres to the style guide
• [x] MD5 sums have been updated
• [x] The PR author has addressed all comments

🗂️ Associated Documentation (to be completed by Theiagen developer)

• [x] Relevant documentation on the Public Health Resources "PHB Main" has been updated
• [x] Workflow diagrams have been updated to reflect changes

[cimendes]

Optional inputs present as expected:

[cimendes]

New outputs present as expected:

[cimendes]

Testing on two identical kraken2 report files here: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/d590d67a-f893-469e-a281-f1126dc13407

[cimendes]

@sage-wright the documentation update is missing for the input and output variables. Do you want to take care of that or should I?

[cimendes]

🌟 Validation worked as expected! 🌟 Approving once documentation is updated!

[sage-wright]

@cimendes, docs have been updated!

[cimendes]

@cimendes, docs have been updated!

Thank you!!! Approving and merging!