update default amrfinderplus docker image to v3.11.20 and db 2023-09-26.1

[kapsakcj]

🛠️ Changes Being Made

updates default docker image for amrfinderplus to us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:3.11.20-2023-09-26.1

This is not the absolute latest version, but the more recent version 3.11.26 only adds a bug fix for a rare bug that does not affect our usage.

More importantly the database has not been updated since 2023-09-26, so we should be pretty up-to-date for the next few months

Impacted Workflows/Tasks

All TheiaProk workflows- ILMN PE, ILMN SE, ONT, FASTA

Standalone amrfinderplus workflow

🧠 Context and Rationale

📋 Workflow/Task Steps

N/A

Inputs

N/A

Outputs

N/A

Impacted Outputs

All outputs will be impacted as results may differ slightly due to database differences

🧪 Testing

Locally

Task ran successfully with miniwdl

Terra

Will add links when testing is complete

• ILMN PE: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/ee39e342-cdeb-4e53-a3ab-1e573fd47522
• ILMN SE: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/287b1378-4aa3-427d-82c2-e6e612b6d32b
• FASTA https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/4d0549c7-70b0-4ada-b113-3c153a38c73c
• ONT: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/6ddb5050-7b00-4ac9-87a7-51ff94b809ae
• standalone amrfinderplus: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/2a34727f-b95f-4118-ab36-7187bfead970

Scenarios for Reviewer to Test

Good to test a variety of different species to try to trigger all of the --organism flag inputs. I have a dataset for doing this with ILMN PE, ILMN SE, and FASTA

My ONT dataset is not comprehensive, it only has a few klebsiella's

🔬 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

[kapsakcj]

Testing in Terra is complete and this PR is ready for review.

Happy to share test datasets with whomever is reviewing, but please throw any and all bacterial samples through the impacted workflows

[frankambrosio3]

Tested here:
TheiaProk_FASTA: https://app.terra.bio/#workspaces/theiagen-validations/ambrosio_validation_sandbox/job_history/8a44e3fb-e18e-4f46-96cd-959b78494616
TheiaProk_Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/ambrosio_validation_sandbox/job_history/c814f7f6-c141-4431-a7ce-bba2193c7cca
TheiaProk_ONT: https://app.terra.bio/#workspaces/theiagen-validations/ambrosio_validation_sandbox/job_history/bdb0d5db-483f-45cb-bd5f-28d5c12f8534
(in ont run, 7 samples hung due to extremely long (>20Mbp) genome size estimation, not due to AMRFinderPlus)