add new location checking script
@@ -47,10 +47,22 @@ rule clean_export_regions:
# Allows 'normal' run of export to be forced to correct lat-long & ordering
# Just runs this, not ZH & GISAID, to speed up & reduce errors.
+# Runs an additional script to give a list of locations that need colors and/or lat-longs
rule export_all_regions:
input:
colors_file = expand("config/colors_{region}.tsv", region=REGIONS),
auspice_json = expand(REGION_PATH + "ncov_with_accessions.json", region=REGIONS),
+ lat_longs = files.lat_longs,
+ metadata = expand("results/metadata_adjusted{region}.tsv", region=REGIONS),
+ colors = expand("config/colors{region}.tsv", region=REGIONS),
+ conda: "../envs/nextstrain.yaml"
+ shell:
+ """
+ python3 ./scripts/check_missing_locations.py \
+ --metadata {input.metadata} \
+ --colors {input.colors} \
+ --latlong {input.lat_longs}
+ """
def _get_sequences_per_group_by_wildcards(wildcards):
if wildcards.region == "global":
