Tree Nine

Put diff files on an existing phylogenetic tree using UShER’s usher sampled task with a bit of help from SRANWRP, followed by conversion to taxonium and Nextstrain/Auspice formats. Auspice sometimes struggles to load a large bacterial phylo tree, so there is the option to output subtrees instead of one very large tree.

Verified on Terra-Cromwell and miniwdl. Make sure to add `–copy-in

This is a companion discussion topic for the original entry at