add reference argument to proximity score
@@ -240,6 +240,7 @@ rule proximity_score:
input:
alignment = rules.mask.output.alignment,
metadata = rules.download.output.metadata,
+ reference = config["files"]["reference"],
focal_alignment = "results/{build_name}/sample-{focus}.fasta"
output:
priorities = "results/{build_name}/proximity_{focus}.tsv"
@@ -252,6 +253,7 @@ rule proximity_score:
"""
python3 scripts/priorities.py --alignment {input.alignment} \
--metadata {input.metadata} \
+ --reference {input.reference} \
--focal-alignment {input.focal_alignment} \
--output {output.priorities} 2>&1 | tee {log}
"""
