adding in --exclude-where date=2020 to augur-filter to remove sequences with no month or day in the collection date
@@ -59,7 +59,8 @@ rule filter:
params:
min_length = 25000,
group_by = "country",
- sequences_per_group = 500
+ sequences_per_group = 500,
+ exclude_where = "date='2020'"
shell:
"""
augur filter \
@@ -67,6 +68,7 @@ rule filter:
--metadata {input.metadata} \
--include {input.include} \
--exclude {input.exclude} \
+ --exclude-where {params.exclude_where}\
--min-length {params.min_length} \
--group-by {params.group_by} \
--sequences-per-group {params.sequences_per_group} \
