[AMRFinderPlus] parse BETA-LACTAM genes and subclasses into individual output columns

[sage-wright]

This PR closes #504.

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

:brain: Aim, Context and Functionality

User requested having the Beta-Lactam AMR genes separated out by all beta-lactam and the respective beta-lactam subclasses.

:hammer_and_wrench: Impacted Workflows/Tasks & Changes Being Made

All TheiaProk workflows now have the option to have the beta-lactam genes parsed out into individual columns and by subclass too.

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Data processing/commands changed:

Beta-Lactam is now parsed into its own columns

➡️ Inputs

• Boolean separate_betalactam_genes

⬅️ Outputs

• String amrfinderplus_amr_betalactam_genes
• String amrfinderplus_amr_betalactam_betalactam_genes
• String amrfinderplus_amr_betalactam_carbapenem_genes
• String amrfinderplus_amr_betalactam_cephalosporin_genes
• String amrfinderplus_amr_betalactam_cephalothin_genes
• String amrfinderplus_amr_betalactam_methicillin_genes

:test_tube: Testing

Test Dataset

TheiaProk_ONT TheiaProk_Illumina_PE

Commandline Testing with MiniWDL or Cromwell (optional)

Terra Testing

Suggested Scenarios for Reviewer to Test

• with separate_betalactam_genes true and false

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

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

🎯 Reviewer Checklist

• [x] All impacted workflows/tasks have been tested on Terra with a different dataset than used for development
• [x] All reviewer-suggested scenarios have been tested and any additional
• [x] 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
• [x] All code adheres to the style guide
• [x] 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

[cimendes]

New outputs present as expected:

separate_betalactam_genes true:

• TheiaProk_ONT: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/b2ad05ef-e3e9-4d7b-85a2-d7f96c2cea55 ✅
• TheiaProk_Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/a1ef2cb1-1cc9-4694-a45f-52dd94b488dd ✅
• TheiaProk_Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/ea07a267-de5c-4068-a5d4-c3933f0abd72 ✅

separate_betalactam_genes false:

• TheiaProk_ONT: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/64bd1e8e-c8d4-4d35-ac8c-d1e8d2c74a11 ✅
• TheiaProk_Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/43e787f0-7478-4d13-9263-2b80976dab2c ✅
• TheiaProk_Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/88ea0e2f-c953-4394-aebc-44a682ac787f ✅