Update tbp-parser Docker and new output

[sage-wright]

Closes

🛠️ Changes Being Made

This PR updates the default tbp-parser Docker image and introduces a new output -- the average depth.

🧠 Context and Rationale

📋 Workflow/Task Steps

Inputs

Outputs

Float tbp_parser_average_genome_depth

🧪 Testing

Locally

Terra

🔬 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

[cimendes]

tbp_parser_average_genome_depth is just an output of the tbp-parser task and is not populated to the theiaprok workflows outputs. Is this as intended?

[sage-wright]

That is not intended

[cimendes]

Testing on Terra:

• TheiaProk_Illumina_PE (n=335): https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/91742a2f-7667-4011-ade7-6d0c1110d2eb
• TheiaProk_Illumina_SE (n=100): https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/54a431c2-32e8-4767-b4e9-14d52e0b711e
• TheiaProk_ONT (n=26): https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/f48faaed-e950-459f-9d78-91b675a49288

The code looks good! I will approve once all the test runs pass and the new output column is correctly populated onto the datatable. :)

[cimendes]

Found a little issue with this branch where very few samples are failing with the following error message:

Bad output 'tbp_parser.tbp_parser_average_genome_depth': Failed to read_float("AVG_DEPTH") (reason 1 of 1): For input string: "-nan"

Job link to an example on Illumina_SE: https://job-manager.dsde-prod.broadinstitute.org/jobs/83f25542-4801-4b15-a3cb-efd0743a591d

Job link to an example on ONT: https://job-manager.dsde-prod.broadinstitute.org/jobs/83f25542-4801-4b15-a3cb-efd0743a591d

The Job links are posted in the comment above this one.

[cimendes]

Retesting with the same datasets on:

• Illumina_PE (fixed issue with wrong docker container being used): https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/8f3333c0-bf59-43e9-bcc9-90be311916cc
• Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/bc8782df-b05d-4528-9b66-fbd916a2f173
• ONT: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/f1c6aaa1-2883-4188-9d72-639a640386e2

[cimendes]

Retesting with commit id 01e1db5:

• Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/7dbb862e-d040-4303-9ad1-fc0e49c5eea8
• Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/0956ebe5-38c4-4d7b-a091-ffe164b7b2bc
• ONT: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/7e5d01f7-4495-4e2b-ad7b-8d92e7a3f82e

[cimendes]

Successful tests for all workflows:

• ONT: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/7131138a-2909-4214-9e67-a12eb7fedfa2
• Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/948360fb-6000-41a0-ae02-b94107547a55
• Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/84f7bafe-b5b4-4c83-bdc6-51290ab02832

Will approve once the CI is happy!