get europe sampling to work
@@ -97,6 +97,7 @@ rule subsample_focus:
region="${{rgn//[_y]/}}"
region="${{region//[-y]/ }}"
grouparg="country year month"
+ echo "Filtering by these groups '$grouparg'"
echo "Filtering for a focal run on $region - $seq_per_group per country"
regionarg="--exclude-where region!="
echo " This is passed to augur as $regionarg'$region'"
@@ -115,7 +116,7 @@ rule subsample_focus:
--metadata {input.metadata} \
--include {input.include} \
$regionarg"$region" \
- --group-by "$grouparg" \
+ --group-by $grouparg \
--sequences-per-group $seq_per_group \
--output {output.sequences} \
