[TheiaProk] update ts_mlst docker image to latest release available (2024-03-11)

[cimendes]

This PR closes #373

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

🧠 Aim, Context and Functionality

This pull request updates ts_mlst docker container to update its database to the latest version available (2024-03-11). This is in preparation for the next release.

🛠️ 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

📋 Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed: Yes, updated to the latest version (2024-03-11)

Databases or database versions changed: Yes, updated to the latest version (2024-03-11)

Data processing/commands changed: None

File processing changed: None

Compute resources changed: None

➡️ Inputs

None were altered.

⬅️ Outputs

None were altered.

🧪 Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

None performed.

Terra Testing

• 20 Samples from multiple species (HAI): https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/0f2b3a48-4742-45a5-901c-1a7b18983282

Suggested Scenarios for Reviewer to Test

Theiagen Version Release Testing (optional)

🔬 Final Developer Checklist

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

🎯 Reviewer Checklist

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

🗂️ Associated Documentation (to be completed by Theiagen developer)

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

[kapsakcj]

This E. coli https://www.ncbi.nlm.nih.gov/sra?LinkName=biosample_sra&from_uid=37796909

is used as a test because we expect the result to be ST15199 which was designated on 2023-10-16 according to: https://pubmlst.org/bigsdb?page=profileInfo&db=pubmlst_escherichia_seqdef&scheme_id=1&profile_id=15199

I'll test this sample along with a number of other species via TheiaProk_FASTA to ensure the new container is used.

Will post the link here shortly

• TheiaProk_FASTA on a lot of different species: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/43797a0d-77e5-411f-a275-2f0bc309da4d
  • outputs look as expected, can see new docker image was used ✅
• TheiaProk_Illumina_PE on the E. coli mentioned above (ST15199): https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/34411022-2886-4d67-b510-2bc083abac30
  • outputs look as expected, ST15199 was observed and new docker image was used ✅

[kapsakcj]

Nice work! Thank you for the PR. You're a ⭐