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nextstrain / mpox

Nextstrain build for mpox virus
https://nextstrain.org/mpox
MIT License
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[phylo] traits input not passed to `augur export` #251

Closed joverlee521 closed 1 month ago

joverlee521 commented 2 months ago

In the phylogenetic workflow, the traits input is not passed to the augur export command --node-data option in the shell.

Looks like this was intentionally removed in https://github.com/nextstrain/mpox/commit/43fdaf1015a5a55b580612308c2b631bc22e9f74 to disable reconstruction of the country field.

This can be confusing for users if they want traits reconstruction for their own analysis.

joverlee521 commented 2 months ago

To get around this, we can move the traits column parameter to be a config parameter. Then conditionalize the traits input for the export rule based on the presence of the config parameter (similar to how the recency input is conditionalized)