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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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[Snippy_Streamline] Add Snippy_variants QC outputs #353

Open emmadoughty opened 4 months ago

emmadoughty commented 4 months ago

:cool:

:pushpin: Explain the Request

Output the Snippy_Variants QC metrics in Snippy_Streamline

:books: Context

The QC metrics in Snippy_Variants (https://github.com/theiagen/public_health_bioinformatics/pull/291) would be very helpful in Snippy_Streamline to determine if all samples should be included in the phylogenetic tree, or if the alignment is poor quality.

:chart_with_upwards_trend: Desired Behavior

Output the Snippy_Variants QC metrics in Snippy_Streamline, either in the Terra table as a list of results and sample names printed next to them for each QC metric, or as a CSV/TSV file to download that contains a table of all QC results, if that is possible!

:information_source: Additional Information