Use metadata id columns from config for epiweeks
When parsing metadata for epiweek annotations, use the user's defined
metadata id columns instead of the defaults for the script.
@@ -1224,10 +1224,13 @@ rule calculate_epiweeks:
config["conda_environment"],
log:
"logs/calculate_epiweeks_{build_name}.txt",
+ params:
+ metadata_id_columns=config["sanitize_metadata"]["metadata_id_columns"],
shell:
"""
python3 scripts/calculate_epiweek.py \
--metadata {input.metadata} \
+ --metadata-id-columns {params.metadata_id_columns:q} \
--output-node-data {output.node_data} 2>&1 | tee {log}
"""
