Breadth (X) of Coverage Column no longer works with aggregate assembly alignment

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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Breadth (X) of Coverage Column no longer works with aggregate assembly alignment #48

Closed Merritt-Brian closed 5 months ago

Merritt-Brian commented 7 months ago

Description of the bug

During Confidence metrics, previously, we call depth on alignment file(s) then indicate how many positions in the chromosome(s) or contigs have an x of coverage. This was broken when pushing the new update for aggregate assemblies.

Command used and terminal output

No response

Relevant files

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System information

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Merritt-Brian commented 5 months ago

Changing how metrics are reported from now on, to be contained in the simplified report