Pathogens not reported as pathogen in report

jhuapl-bio / taxtriage

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.

MIT License

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Pathogens not reported as pathogen in report #63

Closed Merritt-Brian closed 4 months ago

Merritt-Brian commented 5 months ago

Description of the bug

Mismatches in naming of the Refseq post-alignment and pathogen annotation sheet lead to some organisms not being report. Consider 2 options:

More intensive - adding taxid matching in addition to name
Less intensive but a bandaid fix: changing the names directly in the pathogen sheet to the refseq pathogen naming convention

Command used and terminal output

No response

Relevant files

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System information

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Merritt-Brian commented 4 months ago

Completed with commit #8a9d3c976ff77e159ff829b3c3b69d9ddcb33ec1