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Clinical-Genomics-Lund / bonsai

Visualize and analyze resistance and outbreak of bacterial pathogen
https://bonsai-wgs.readthedocs.io/en/latest/
GNU General Public License v3.0
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Add export sample to LIMS command #147

Closed mhkc closed 8 months ago

mhkc commented 9 months ago

This PR adds a command to the Bonsai API for exporting a sample to a LIMS compatible format.

The PR also add basic unit tests for the function and two example inputs from PRP.

How to setup and perform the tests

  1. Setup Bonsai and load the two included test input files.
  2. Log into the API docker container
  3. Try export test_mtuberculosis_1 (bonsai_api export -i test_mtuberculosis_1)
mhkc commented 9 months ago

Rebuild passes. Was just some random ReadTheDocs error