Add kraken2 species prediction results to sample view and fix cmlst missing alleles - Githubissues

Clinical-Genomics-Lund / bonsai

Visualize and analyze resistance and outbreak of bacterial pathogen

https://bonsai-wgs.readthedocs.io/en/latest/

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Add kraken2 species prediction results to sample view and fix cmlst missing alleles #104

Closed mhkc closed 10 months ago

mhkc commented 10 months ago

This PR adds a specie prediction card to the sample view in Bonsai frontend and fixes the calculation of the number of cgmlst alleles.

closes #101 #100

How to setup and perform the tests

step bonsai and load a sample to the database
goto the sample view

sample with one predicted spp, http://mtlucmds2.lund.skane.se:8812/samples/11MT0500255 sample with two predicted spp, http://mtlucmds2.lund.skane.se:8812/samples/11MT0500122

Expected outcome

The species prediction result should be displayed and understandable.
The correct number of cgmlst alleles should be displayed.