Dynamically generate the auspice config files - #45
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Instead of maintaining 5 auspice config files, we can generate them. This becomes more important as we support gene builds (e.g. supporting "genome" and "E" gene builds will result in 10 auspice config files).
Coloring the tree based on the Nextclade genotype assignments as well as the "augur clades" call allows for debugging and validation of the Nextclade dataset.
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The "Nextclade genotype" annotation was being displayed out of order in the color scheme. This commit adds a color ordering file that can be used to specify the order of colors for nextclade_genotype, country, region, and recency. This was copied and modified from the "colors" rule in RSV's workflow * https://github.com/nextstrain/rsv/blob/a1788ce2c9c4375fb5a06d1426c64c45cf90225f/workflow/snakemake_rules/export.smk#L13-L27
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Going to merge this PR, to unblock rebasing and working on #18 Post-merge review still welcome |
This was referenced Apr 30, 2024
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Description of proposed changes
As requested here: #18 (comment) , 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)
#18
Checklist