Retry NCBI Reference Pulls

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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Retry NCBI Reference Pulls #40

Closed Merritt-Brian closed 7 months ago

Merritt-Brian commented 10 months ago

Description of feature

Currently, the NCBI reference pull step for an assembly for each taxa only happens once. If it fails it skips. Can we do a re-attempt somewhere around here: https://github.com/jhuapl-bio/taxtriage/blob/main/bin/download_fastas.py#L257