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nextstrain / dengue

Nextstrain build for dengue virus
https://nextstrain.org/dengue
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Dynamically generate the auspice config files #45

Closed j23414 closed 2 months ago

j23414 commented 2 months ago

Description of proposed changes

As requested here: https://github.com/nextstrain/dengue/pull/18#discussion_r1454394060 , implemented dynamic generation of the Auspice config files.

Additionally, included "Nextclade genotype" coloring to the the tree, which will help with dataset validation and debugging.

Related issue(s)

https://github.com/nextstrain/dengue/pull/18

Checklist

j23414 commented 2 months ago

Tested the phylogenetic workflow (using dynamically generated auspice files) from a GitHub Action (Phylogenetic): https://github.com/nextstrain/dengue/actions/runs/8852723611

The results are on staging and can be viewed below: all | denv1 | denv2 | denv3 | denv4

j23414 commented 2 months ago

After fixing the color order (https://github.com/nextstrain/dengue/pull/45/commits/86d9641f1c3a120ed5b5672b085dc547e9aaa1ba) and rerunning phylogenetic, the fixed results can be viewed below:

all | denv1 | denv2 | denv3 | denv4

j23414 commented 2 months ago

Going to merge this PR, to unblock rebasing and working on https://github.com/nextstrain/dengue/pull/18

Post-merge review still welcome