I don't think this is part of the scope of this PR, but it would seem cleaner to me for this clade-labeling/add-clades.py script to instead just create a node data JSON with h5_label_clade rather than messing with the metadata file.
@lmoncla and I just had some confusion from different rules (refine, traits) asking for the metadata TSV vs the metadata-with-clade TSV. Though the function metadata_by_wildcards mostly solves this issue.
@jameshadfield noted that:
The only reason I can see to not do this is if we use this data in the filtering step. But we don't.
Description
We should modify scripts/add-clades.py to create a node data JSON file as output and update the workflow to make the resulting output an input to the export rule instead of a step that modifies the metadata.
Context
In conversation about #22, @trvrb noted:
@jameshadfield noted that:
Description
We should modify
scripts/add-clades.pyto create a node data JSON file as output and update the workflow to make the resulting output an input to theexportrule instead of a step that modifies the metadata.