Don't exclude outliers from reference subsamples

Removes the `--exclude` argument from reference subsamples in all builds
to prevent a bug where a strain can be listed in a lineage's
"references" file and also (accidentally) listed in the lineage's
outliers file leading references to be excluded when they should be
force-included. This commit removes the outlier filter from "references"
subsample blocks across all build configs.

profiles/nextflu-private-forecasts.yaml

@@ -84,7 +84,7 @@ array-builds:
       europe:
           filters: --query "(passage_category != 'egg') & (region == 'Europe')" --group-by country year month --subsample-max-sequences 150 --min-date {min_date} --exclude {exclude}
       references:
-          filters: --query "(passage_category != 'egg') & (is_reference == True)" --min-date {reference_min_date} --exclude {exclude}
+          filters: --query "(passage_category != 'egg') & (is_reference == True)" --min-date {reference_min_date}
       titer_strains:
           filters: --query "(passage_category != 'egg') & (is_titer_strain == True)" --group-by region year month --subsample-max-sequences 350 --min-date 1Y --exclude {exclude}
           priorities: "titers"

profiles/nextflu-private.yaml

@@ -92,7 +92,7 @@ builds:
           filters: --query "(passage_category != 'egg') & (region == 'Europe') & (ha == True) & (na == True)" --group-by country year month --subsample-max-sequences 300 --min-date {min_date} --exclude {exclude}
           priorities: "titers"
       references:
-          filters: --query "(is_reference == True)" --min-date {reference_min_date} --exclude {exclude}
+          filters: --query "(is_reference == True)" --min-date {reference_min_date}
       titer_strains:
           # We allow egg-passage strains when they have titer measurements,
           # enabling titer models to be fit to egg-passaged data.
@@ -203,7 +203,7 @@ builds:
           filters: --query "(passage_category != 'egg') & (region == 'Europe') & (ha == True) & (na == True)" --group-by country year month --subsample-max-sequences 300 --min-date {min_date} --exclude {exclude}
           priorities: "titers"
       references:
-          filters: --query "(is_reference == True)" --min-date {reference_min_date} --exclude {exclude}
+          filters: --query "(is_reference == True)" --min-date {reference_min_date}
   h3n2_2y:
     lineage: "h3n2"
     reference: "config/h3n2/{segment}/reference.fasta"

profiles/nextflu-public.yaml

@@ -85,7 +85,7 @@ builds:
       context:
           filters: --query "(passage_category != 'egg')" --group-by region year --subsample-max-sequences 300 --max-date 2020-03-01 --min-date 2016-01-01 --exclude {exclude}
       references:
-          filters: --query "(passage_category != 'egg') & (is_reference == True)" --min-date {reference_min_date} --exclude {exclude}
+          filters: --query "(passage_category != 'egg') & (is_reference == True)" --min-date {reference_min_date}
   h3n2_2y:
     lineage: "h3n2"
     reference: "config/h3n2/{segment}/reference.fasta"

profiles/nextstrain-public-yamagata.yaml

@@ -84,7 +84,7 @@ array-builds:
           filters: --query "(passage_category != 'egg') & (region == 'Europe') & (ha == True) & (na == True)" --group-by country year month --subsample-max-sequences 300 --min-date {min_date} --max-date {max_date} --exclude {exclude}
           priorities: "titers"
       references:
-          filters: --query "(is_reference == True)" --min-date {reference_min_date} --max-date {max_date} --exclude {exclude}
+          filters: --query "(is_reference == True)" --min-date {reference_min_date} --max-date {max_date}
   2Y-hi-builds:
     patterns:
       lineage:

profiles/nextstrain-public.yaml

@@ -83,7 +83,7 @@ array-builds:
           filters: --query "(passage_category != 'egg') & (region == 'Europe') & (ha == True) & (na == True)" --group-by country year month --subsample-max-sequences 300 --min-date {min_date} --exclude {exclude} --exclude-where passage=egg
           priorities: "titers"
       references:
-          filters: --query "(is_reference == True)" --min-date {reference_min_date} --exclude {exclude} --exclude-where passage=egg
+          filters: --query "(is_reference == True)" --min-date {reference_min_date} --exclude-where passage=egg
   2Y-hi-builds:
     patterns:
       lineage:

profiles/private.nextflu.org.yaml

@@ -89,7 +89,7 @@ array-builds:
           filters: --query "(passage_category in ['{passage}', 'cell', 'unpassaged', 'undetermined', 'N/A']) & (region == 'Europe')" --group-by country year month --subsample-max-sequences 300 --min-date {min_date} --exclude {exclude} --exclude-where country=? region=?
           priorities: "titers"
       references:
-          filters: --query "(is_reference == True)" --min-date {reference_min_date} --exclude {exclude}
+          filters: --query "(is_reference == True)" --min-date {reference_min_date}
   6Y-hi-builds:
     patterns:
       center:

profiles/upload.yaml

@@ -109,7 +109,7 @@ builds:
       context:
           filters: --query "(passage_category != 'egg')" --group-by region year --subsample-max-sequences 300 --max-date 2020-03-01 --min-date 2016-01-01 --exclude {exclude}
       references:
-          filters: --query "(passage_category != 'egg') & (is_reference == True)" --min-date {reference_min_date} --exclude {exclude}
+          filters: --query "(passage_category != 'egg') & (is_reference == True)" --min-date {reference_min_date}
   h3n2_2y:
     lineage: "h3n2"
     reference: "config/h3n2/{segment}/reference.fasta"