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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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Output whole genome SNP matrix for Snippy_Streamline and Snippy_Tree workflows even when core_genome used #339

Closed emmadoughty closed 4 months ago

emmadoughty commented 4 months ago

:cool:

:pushpin: Explain the Request

Output whole genome SNP matrix for Snippy_Streamline and Snippy_Tree workflows when core_genome = true is used, in addition to the core-genome SNP matrix

:books: Context

Knowing pairwise wgSNP distances is critical for assessing epi relationships, even when a core-genome tree is used. Currently, users have to run Snippy_Streamline/Tree twice to get both a core tree and whole-genome SNP matrix, which is a bit cumbersome

:chart_with_upwards_trend: Desired Behavior

Provide wgSNP matrix regardless of whether core or whole genome tree is made (in addition to cgSNP matrix if core_genome is used)

:information_source: Additional Information