Update IRMA Module Output Settings and Modify Abricate_flu Module for Specific Flu B Classification

[tives82]

This pull request introduces two changes that improve the file outputs of the IRMA module and enhance the flu B lineage classification in the Abricate_flu module.

1. IRMA Module Output Modification: The outputs for BAM and FASTA files have been updated to optional: true. This will ensure that any absence of output BAM and/or FASTA files during IRMA module execution does not cause the process to halt or fail, addressing issues related to missing output files in certain scenarios.

2. Syntax Update for the Abricate_flu Module: Introduces a better approach to classifying flu B viruses by focusing specifically on the hemagglutinin (HA) and neuraminidase (NA) segments for flu B lineage determination. The revised code now includes a conditional logic to identify the flu B virus as either Victoria or Yamagata lineage based on the presence of HA and NA markers in the abricate output. The updated script checks for the presence of "Type_B" in the classification output and then proceeds to determine the subtype by searching for "Victoria" or "Yamagata" in conjunction with "hemagglutinin" or "neuraminidase". The logic is as follows: if either HA or NA markers, or both, are found in conjunction with "Type B" in the ${meta.id}_abricate_hits.tsv file, the script assigns the respective subtype.
   This modification improves the accuracy of flu B lineage classification by relying on the HA and NA segments, which are the indicators of the flu B lineage, and addresses a previous limitation where lineage assignment might have been inaccurately influenced by non-specific markers such as matrix proteins (MP).

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 565cbb5

+| ✅  16 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

• files_exist - files_exist
• nextflow_config - nextflow_config
• files_unchanged - files_unchanged
• actions_awstest - actions_awstest
• multiqc_config - multiqc_config
• modules_structure - modules_structure

✅ Tests passed:

• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
• readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (127 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json

Run details

• nf-core/tools version 2.7.2
• Run at 2024-04-09 20:53:05

[erinyoung]

Is https://github.com/UPHL-BioNGS/walkercreek/blob/master/.devcontainer/devcontainer.json supposed to be a real json file or a pseudo-json file? If it's supposed to be a real json file, there are some extra commas.

[jwarnn]

I see no issue with these file changes and test run completed successfully.