Update IRMA Module Output Settings and Modify Abricate_flu Module for Specific Flu B Classification #10
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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.
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.
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).