exclude bad sequences at subsampling step
@@ -399,7 +399,8 @@ rule subsample:
sequences = "results/masked.fasta",
metadata = config["metadata"],
include = config["files"]["include"],
- priorities = get_priorities
+ priorities = get_priorities,
+ exclude = config["files"]["exclude"]
output:
sequences = "results/{build_name}/sample-{subsample}.fasta"
log:
@@ -421,6 +422,7 @@ rule subsample:
--sequences {input.sequences} \
--metadata {input.metadata} \
--include {input.include} \
+ --exclude {input.exclude} \
{params.min_date} \
{params.max_date} \
{params.exclude_argument} \
