make traits listen to config
@@ -405,11 +405,11 @@ rule traits:
tree = rules.refine.output.tree,
metadata = _get_metadata_by_wildcards
output:
- node_data = REGION_PATH + "traits.json",
+ node_data = REGION_PATH + "traits.json"
params:
- columns = _get_exposure_trait_for_wildcards,
- sampling_bias_correction = config["traits"]["sampling_bias_correction"]
- conda: config["conda_environment"]
+ columns = lambda w: config["traits"][w.region]["columns"],
+ sampling_bias_correction = lambda w: config["traits"][w.region]["sampling_bias_correction"]
+ conda: "../envs/nextstrain.yaml"
shell:
"""
augur traits \
