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Copies the Nextclade "subclade" column to a new "subclade_nextclade" field and adds this new column to the Auspice config JSON for H3N2 HA as a proof of concept for exporting Nextclade-based clade annotations alongside the `augur clades` annotations. Since the Nextclade annotation of subclade already exists in the metadata we pass to `augur export`, we just need to rename that column to avoid conflicting with the "subclade" attribute that also appears in the node data JSON inputs to `augur export`. To avoid breaking any downstream logic that relies on the Nextclade column name of "subclade", I've chosen to duplicate the original column to a new column with the desired name. Related to #254 Related to #131
This was referenced Oct 2, 2025
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Description of proposed changes
Copies the Nextclade "subclade" column to a new "subclade_nextclade" field and adds this new column to the Auspice config JSON for H3N2 HA as a proof of concept for exporting Nextclade-based clade annotations alongside the
augur cladesannotations. Since the Nextclade annotation of subclade already exists in the metadata we pass toaugur export, we just need to rename that column to avoid conflicting with the "subclade" attribute that also appears in the node data JSON inputs toaugur export. To avoid breaking any downstream logic that relies on the Nextclade column name of "subclade", I've chosen to duplicate the original column to a new column with the desired name.This approach could be a simple first step toward the complete replacement of
augur cladeswith Nextclade as described in #131. This approach does not try to solve the issue of assigning clade labels to internal nodes or creating branch labels for clades.Related issue(s)
Related to #254
Related to #131
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