Update workflow for new augur clades version by jameshadfield · Pull Request #1000 · nextstrain/ncov (original) (raw)
This updates the workflow to use the new clades interface from augur v22 (see nextstrain/augur#728). In the process we can remove two rules from the workflow. The minimum augur version is bumped to 22.0.1, as that includes a couple of important bug-fixes.
If this workflow is run with augur prior to v22, the emerging_lineages rule will error due to unknown arguments.
The script add_branch_labels.py is no longer used and thus removed here (as recommended in code review: #1000 (comment)) Note that it contained unused functionality to export spike mutations; if we reinstate this in the future we should update the output format to produce a node-data JSON with a custom branch label to avoid modifying the auspice JSON after export.
This is a minor aesthetic change which restores the order of the
branch labels in Auspice so that clade appears before emerging_lingeage.
The change in ordering was introduced by the previous commit as
we moved from a custom script to using augur clades interface from
Augur v22.0.0
The ordering is not specified and cannot be configured, but in practice it is the order of the keys in the dictionary (and which is stable in CPython 3.6, Python 3.7, and most (all?) JS engines).
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