explicity specify diagnostic parameters
@@ -97,11 +97,14 @@ rule align:
"""
rule diagnostic:
- message: "Scanning metadata {input.metadata} for problematic sequences"
+ message: "Scanning metadata {input.metadata} for problematic sequences. Removing sequences with >{params.clock_filter} deviation from the clock and with more than {params.snp_clusters}."
input:
metadata = "results/sanitized_metadata_{origin}.tsv.xz"
output:
to_exclude = "results/to-exclude_{origin}.txt"
+ params:
+ clock_filter = 20,
+ snp_clusters = 1
log:
"logs/diagnostics_{origin}.txt"
benchmark:
@@ -114,6 +117,8 @@ rule diagnostic:
"""
python3 scripts/diagnostic.py \
--metadata {input.metadata} \
+ --clock-filter {params.clock_filter} \
+ --snp-clusters {params.snp_clusters} \
--output-exclusion-list {output.to_exclude} 2>&1 | tee {log}
"""
