update docker to version tag 2.23.0-2024-01

[cimendes]

Closes #262

🛠️ Changes Being Made

Impacted Workflows/Tasks

All Theiaprok workflows

• TheiaProk_Illumina_PE
• TheiaProk_Illumina_SE
• TheiaProk_ONT
• TheiaProk_FASTA

🧠 Context and Rationale

This PR updates the mlst database sync with pubmlst as of January 2024

New docker container: us-docker.pkg.dev/general-theiagen/staphb/mlst:2.23.0-2024-01

📋 Workflow/Task Steps

N/A

Inputs

N/A

Outputs

N/A

Impacted Outputs

All mlst outputs

    File? ts_mlst_results = ts_mlst.ts_mlst_results
    String? ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st
    String? ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme
    String? ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile
    String? ts_mlst_version = ts_mlst.ts_mlst_version
    File? ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles
    String? ts_mlst_docker = ts_mlst.ts_mlst_docker

🧪 Testing

Locally

Local test passed with no issue on the mlst task

Terra

Underway

• TheiaProk_FASTA_PHB: 5 K. pneumoniae (https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/28eb3ff4-9c8b-4413-a373-b172d43a4fd1)

Scenarios for Reviewer to Test

All mlst calls are accurate with pubmlst database as of January 2024

🔬 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

[kevinlibuit]

Thanks for the quick PR! Changes look great and this is ready for merging to main.

@kapsakcj wondering if we also want to mimic this practice for staphb images, i.e. creating mlst docker images with updated db. Hah, this conversation of docker-builds and dynamic databases continues!

[kapsakcj]

@kapsakcj wondering if we also want to mimic this practice for staphb images, i.e. creating mlst docker images with updated db. Hah, this conversation of docker-builds and dynamic databases continues!

Yes, I think it would be good to update the mlst docker image on a schedule, perhaps once a month. Let's chat about this at the next staphb/docker-builds dev meeting

[cimendes]

The documentation has been updated to reflect this merge!