fix: set cutoff for rare mutations to a high value, effectively disabling this filter
@@ -104,7 +104,8 @@ rule diagnostic:
to_exclude = "results/to-exclude_{origin}.txt"
params:
clock_filter = 20,
- snp_clusters = 1
+ snp_clusters = 1,
+ rare_mutations = 100,
log:
"logs/diagnostics_{origin}.txt"
benchmark:
@@ -118,6 +119,7 @@ rule diagnostic:
python3 scripts/diagnostic.py \
--metadata {input.metadata} \
--clock-filter {params.clock_filter} \
+ --rare-mutations {params.rate_mutations} \
--snp-clusters {params.snp_clusters} \
--output-exclusion-list {output.to_exclude} 2>&1 | tee {log}
"""
