TheiaCoV_ONT_PHB Influenza Track

[jrotieno]

Closes N/A

🛠️ Changes Being Made

This PR adds an Influenza track onto the TheiaCoV_ONT_PHB workflow.

Uses the same IRMA task that performs assembly of influenza viruses but with module specification for ONT reads.

Impacted Workflows/Tasks

• TheiaCoV_ONT_PHB
• TheiaCoV_Illumina_PE
• IRMA task

🧠 Context and Rationale

Many public health laboratories are increasingly generating Oxford Nanopore data, hence the need for an influenza track to handle such inputs within

📋 Workflow/Task Steps

Inputs

Required inputs are:
read1
samplename

Recommended optional inputs:
organism - Required when analyzing pathogens other than SARS-CoV-2, e.g. "HIV" and "flu"
primer_bed - Was previously a required input, now an optional input as not required for flu analysis. However, it is required for other pathogens processed by the workflow such as HIV and SARS-CoV-2
reference_genome also required for HIV analysis

Outputs

Impacted Outputs

Additional outputs added are:
irma_version
irma_type
irma_subtype
irma_ha_segment
irma_na_segment
abricate_flu_type
abricate_flu_subtype
abricate_flu_results
abricate_flu_database
abricate_flu_version

🧪 Testing

Locally

Works as expected

Terra

Works as expected.
SARS-CoV-2: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/e485251a-be75-497e-be95-7ed6368071f8
HIV: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/e5dcd4b7-aa91-4057-9290-b5267433a3f2
Flu H1N1: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/7a136cfd-e05c-4a8e-927c-78bd36c37514

Scenarios for Reviewer to Test

Test with H3N2 and cases that would fail QC for other pathogens

🔬 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

[frankambrosio3]

Tested here on 15 flu samples from NCBI: https://app.terra.bio/#workspaces/theiagen-validations/ambrosio_validation_sandbox/job_history/281314c6-d856-4010-ae93-dd746045a235

[sage-wright]

Rerunning ONT flu so outputs are produced: https://app.terra.bio/#workspaces/theiagen-validations/ambrosio_validation_sandbox/job_history/014607f3-9571-4013-873c-634e709def3a

ONT HIV: https://app.terra.bio/#workspaces/theiagen-validations/ambrosio_validation_sandbox/job_history/eb34434a-c61d-476c-814b-6025dc2bfda4

Illumina_PE flu: https://app.terra.bio/#workspaces/theiagen-validations/ambrosio_validation_sandbox/job_history/b8448a5b-234d-4f5b-b074-b15bd9fe3eb2

Illumina_PE sc2: https://app.terra.bio/#workspaces/theiagen-validations/ambrosio_validation_sandbox/job_history/314b1332-0a70-47f8-adbd-3050e3e44bfb