add divergence unit argument, root on early Wuhan case
@@ -176,7 +176,8 @@ rule refine:
clock_rate = 0.00035,
clock_std_dev = 0.00015,
coalescent = "skyline",
- date_inference = "marginal"
+ date_inference = "marginal",
+ divergence_unit = "mutations"
shell:
"""
augur refine \
@@ -191,6 +192,7 @@ rule refine:
--clock-std-dev {params.clock_std_dev} \
--coalescent {params.coalescent} \
--date-inference {params.date_inference} \
+ --divergence-unit {params.divergence_unit} \
--date-confidence \
--no-covariance
"""
