Adds Vibecheck to the Vibrio spp. subworkflow of TheiaProk

[watronfire]

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

🧠 Summary

This PR adds a additional task to the Vibrio spp. subworkflow of TheiaProk which runs Vibecheck. Vibecheck rapidly classifies V. cholerae sequencing data to canonical lineages (T1-T17/AFR1-AFR17).

⚡ Impacted Workflows/Tasks

• TheiaProk_Illumina_PE
• merlin_magic

This PR may lead to different results in pre-existing outputs: No

This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

This PR adds an additional task task_vibecheck_vibrio.wdl, which is called during Vibrio spp. branch of the merlin_magic workflow. Therefore, the inputs, parameters, and outputs of the additional task were added to wf_merlin_magic.wdl and wf_theiaprok_illumina_pe.wdl

⚙️ Algorithm

No changes were made to existing algorithms or processes. However, inputs, parameters, and outputs were added for the Vibecheck task.

➡️ Inputs

The following inputs were added. All are optional.

• String vibecheck_lineage_barcode
• Float vibecheck_subsampling_fraction
• Boolean vibecheck_skip_subsampling
• String vibecheck_docker_image

⬅️ Outputs

The following outputs were added:

• File vibecheck_lineage_report
• String vibecheck_top_lineage
• Float vibecheck_confidence
• String vibecheck_classification_notes
• String vibecheck_version
• String vibecheck_docker

🧪 Testing

I've manually tested a similar task in the Vibecheck Github repo. However, I'm unclear how exactly to test this specific task locally. Any advise or recommendations you have would be much appreciated.

Suggested Scenarios for Reviewer to Test

Success and accuracy of classification should be tested. I can provide raw data for cholera isolates with known lineage classifications if it's helpful.

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (Theiagen developers)
• Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable
  • You have updated the "Last Known Changes" field for any affected workflows in the respective workflow documentation page and for every entry in the three workflows_overview tables to be the tag for the next upcoming release. If you do not know the tag, please put "vX.X.X"

🎯 Reviewer Checklist

• All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated

[sage-wright]

Thank you so much for this PR! We'll take a look at it and run it through our tests this week. I'm excited to take a look at this one!

[sage-wright]

Thank you so much @watronfire! This PR looks fantastic, and my tests showed everything was implemented correctly. This is a fantastic add!
⭐