Restore inclusion of title
@@ -440,6 +440,28 @@ rule export:
auspice_json = "results/ncov_with_accessions{region}.json"
shell:
"""
+ #Figure out what region being wanted
+ rgn="{wildcards.region}"
+
+ # Catch in case a run with no wild card (just in case)
+ # Catch case for global build
+ # else, remove - and capitalize
+ if [ -z "$rgn" ]; then
+ regioncap=""
+ title="Genomic epidemiology of novel coronavirus"
+ elif [ "$rgn" = "_global" ]; then
+ regioncap="Global"
+ title="Genomic epidemiology of novel coronavirus - Global subsampling"
+ else
+ region="${{rgn//[_y]/}}"
+ region="${{region//[-y]/ }}"
+ regionlist=( $region )
+ regioncap="${{regionlist[@]^}}"
+ title="Genomic epidemiology of novel coronavirus - $regioncap-focused subsampling"
+ fi
+
+ echo "region is $regioncap"
+
augur export v2 \
--tree {input.tree} \
--metadata {input.metadata} \
@@ -447,6 +469,7 @@ rule export:
--auspice-config {input.auspice_config} \
--colors {input.colors} \
--lat-longs {input.lat_longs} \
+ --title "$title" \
--description {input.description} \
--output {output.auspice_json}
"""
