Additional Updates to Flu antiviral Calls in TheiaCoV Workflows

This PR closes #356

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

:brain: Aim, Context and Functionality

This PR adds checks for mutations that confer resistance to Amantadine and Rimantadine to all TheiaCoV workflows, and adds all antiviral checks previously implemented for Illumina into TheaiCoV ONT.

:hammer_and_wrench: 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 : Yes

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

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed: N/A

Databases or database versions changed: N/A

Data processing/commands changed:

File processing changed: Added reference files for M2 protein and steps to check for antiviral resistance to Amantadine and Rimantadine.

Compute resources changed: N/A

➡️ Inputs

No additional inputs for the TheiaCoV workflows

⬅️ Outputs

For TheiaCoV_illumina_PE_PHB:

    flu_amantadine_resistance
    flu_rimantadine_resistance

For TheiaCoV_ONT_PHB:

    flu_A_315675_resistance
    flu_amantadine_resistance
    flu_compound_367_resistance
    flu_favipiravir_resistance
    flu_fludase_resistance
    flu_L_742_001_resistance
    flu_laninamivir_resistance
    flu_peramivir_resistance
    flu_pimodivir_resistance
    flu_rimantadine_resistance
    flu_oseltamivir_resistance
    flu_xofluza_resistance
    flu_zanamivir_resistance

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Not undertaken

Terra Testing

Illumina reads: A set of four samples were used, Yamagata, H3N2 and H1N1. One with low quality, but workflow expected to run to the end. https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/cc37bf3f-3bdb-43e1-aebb-499d2aa5be6d

ONT: A set of five samples with varied levels of sequence quality, with some expected to fail assembly (a fix was implemented on a different branch to allow workflow to proceed to the end when assembly fails). All H1N1. https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/09368ebf-cad9-4e99-8d6c-846a7f30171d

Suggested Scenarios for Reviewer to Test

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

[X] 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

[ ] 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
[X] Workflow diagrams have been updated to reflect changes

theiagen / public_health_bioinformatics