Github.com/aofarrel/tree_nine/summarize_usher_tree

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 github.com/aofarrel/tree_nine/summarize_usher_tree