Add clade definition for 24C

config/config.yaml

@@ -1,147 +1,147 @@
-# See ingest/README.md for all available data
-data_provenances:
-  - gisaid
-  - open
-variant_classifications:
-  - nextstrain_clades
-  - pango_lineages
-geo_resolutions:
-  - global
-
-# Params for the prepare data scripts
-# Define params for each data_provenance / variant_classification / geo_resolution combination
-# Include `max_date` if you don't want to use today as the max date
-prepare_data:
-  gisaid:
-    nextstrain_clades:
-      global:
-        included_days: 150
-        location_min_seq: 50
-        location_min_seq_days: 30
-        excluded_locations: "defaults/global_excluded_locations.txt"
-        prune_seq_days: 12
-        clade_min_seq: 2000
-        clade_min_seq_days: 150
-    pango_lineages:
-      global:
-        included_days: 150
-        location_min_seq: 150
-        location_min_seq_days: 30
-        excluded_locations: "defaults/global_excluded_locations.txt"
-        prune_seq_days: 12
-        clade_min_seq: 1
-        clade_min_seq_days: 150
-        collapse_threshold: 350
-  open:
-    nextstrain_clades:
-      global:
-        included_days: 150
-        location_min_seq: 50
-        location_min_seq_days: 30
-        excluded_locations: "defaults/global_excluded_locations.txt"
-        prune_seq_days: 12
-        clade_min_seq: 2000
-        clade_min_seq_days: 150
-    pango_lineages:
-      global:
-        included_days: 150
-        location_min_seq: 150
-        location_min_seq_days: 30
-        excluded_locations: "defaults/global_excluded_locations.txt"
-        prune_seq_days: 12
-        clade_min_seq: 1
-        clade_min_seq_days: 150
-        collapse_threshold: 350
-
-# Params for the model run scripts
-models:
-  gisaid:
-    nextstrain_clades:
-      global:
-        pivot: "24A"
-    pango_lineages:
-      global:
-        pivot: "JN.1"
-  open:
-    nextstrain_clades:
-      global:
-        pivot: "24A"
-    pango_lineages:
-      global:
-        pivot: "JN.1"
-
-# Model configs
-mlr_config: "config/mlr-config.yaml"
-# don't run renewal model by default
-#renewal_config: "config/renewal-config.yaml"
-
-
-# A mapping between nextstrain clades, defining pango lineages and clade colours.
-# Colours will be assigned to pango lineages by first associating it with its
-# corresponding nextstrain clade and then interpolating colours close to the
-# clade's colour; this allows each individual lineage to have its own colour
-# whilst being able to visually associate them back to their nextstrain clade.
-#
-# The order in the list must be hierarchical w.r.t pango lineages, i.e. XBB.1.9
-# must appear _before_ XBB
-#
-# NOTES:
-# * Lineages are ordered (in the legend & for the GA estimates) alphabetically
-#   via their full pango name. This doesn't map nicely onto nextstrain clade
-#   definitions, which is why an individual colour scale defined here may appear
-#   in multiple parts of the graph.
-# * Lineages which are not a descendant of a clade-defining lineage will be
-#   grouped as 'other'
-clade_definitions:
-  - clade: "24B"
-    display_name: "24B (JN.1.11.1)"
-    defining_lineage: "JN.1.11.1"
-    color: '#DC2F24'
-  - clade: "24A"
-    display_name: "24A (JN.1)"
-    defining_lineage: "JN.1"
-    color: '#E4632E'
-  - clade: "23I"
-    display_name: "23I (BA.2.86)"
-    defining_lineage: "BA.2.86"
-    color: '#E69136'
-  - clade: "23H"
-    display_name: "23H (HK.3)"
-    defining_lineage: "HK.3"
-    color: '#D9AD3D'
-  - clade: "23G"
-    display_name: "23G (XBB.1.5.70)"
-    defining_lineage: "XBB.1.5.70"
-    color: '#C1BA47'
-  - clade: "23F"
-    display_name: "23F (EG.5.1)"
-    defining_lineage: "EG.5.1"
-    color: '#A2BE57'
-  - clade: "23E"
-    display_name: "23E (XBB.2.3)"
-    defining_lineage: "XBB.2.3"
-    color: '#83BA70'
-  - clade: "23D"
-    display_name: "23D (XBB.1.9)"
-    defining_lineage: "XBB.1.9"
-    color: '#69B091'
-  - clade: "23C"
-    display_name: "23C (CH.1.1)"
-    defining_lineage: "CH.1.1"
-    color: '#549DB2'
-  - clade: "23B"
-    display_name: "23B (XBB.1.16)"
-    defining_lineage: "XBB.1.16"
-    color: '#4580CA'
-  - clade: "22F"
-    display_name: "22F (XBB)"
-    defining_lineage: "XBB"
-    color: '#3E58CF'
-  - clade: "23A"
-    display_name: "23A (XBB.1.5)"
-    defining_lineage: "XBB.1.5"
-    color: '#462EB9'
-  - clade: "other"
-    display_name: "other"
-    defining_lineage: False
-    color: '#777777'
+# See ingest/README.md for all available data
+data_provenances:
+  - gisaid
+  - open
+variant_classifications:
+  - nextstrain_clades
+  - pango_lineages
+geo_resolutions:
+  - global
+
+# Params for the prepare data scripts
+# Define params for each data_provenance / variant_classification / geo_resolution combination
+# Include `max_date` if you don't want to use today as the max date
+prepare_data:
+  gisaid:
+    nextstrain_clades:
+      global:
+        included_days: 150
+        location_min_seq: 50
+        location_min_seq_days: 30
+        excluded_locations: "defaults/global_excluded_locations.txt"
+        prune_seq_days: 12
+        clade_min_seq: 2000
+        clade_min_seq_days: 150
+    pango_lineages:
+      global:
+        included_days: 150
+        location_min_seq: 150
+        location_min_seq_days: 30
+        excluded_locations: "defaults/global_excluded_locations.txt"
+        prune_seq_days: 12
+        clade_min_seq: 1
+        clade_min_seq_days: 150
+        collapse_threshold: 350
+  open:
+    nextstrain_clades:
+      global:
+        included_days: 150
+        location_min_seq: 50
+        location_min_seq_days: 30
+        excluded_locations: "defaults/global_excluded_locations.txt"
+        prune_seq_days: 12
+        clade_min_seq: 2000
+        clade_min_seq_days: 150
+    pango_lineages:
+      global:
+        included_days: 150
+        location_min_seq: 150
+        location_min_seq_days: 30
+        excluded_locations: "defaults/global_excluded_locations.txt"
+        prune_seq_days: 12
+        clade_min_seq: 1
+        clade_min_seq_days: 150
+        collapse_threshold: 350
+
+# Params for the model run scripts
+models:
+  gisaid:
+    nextstrain_clades:
+      global:
+        pivot: "24A"
+    pango_lineages:
+      global:
+        pivot: "JN.1"
+  open:
+    nextstrain_clades:
+      global:
+        pivot: "24A"
+    pango_lineages:
+      global:
+        pivot: "JN.1"
+
+# Model configs
+mlr_config: "config/mlr-config.yaml"
+# don't run renewal model by default
+#renewal_config: "config/renewal-config.yaml"
+
+
+# A mapping between nextstrain clades, defining pango lineages and clade colours.
+# Colours will be assigned to pango lineages by first associating it with its
+# corresponding nextstrain clade and then interpolating colours close to the
+# clade's colour; this allows each individual lineage to have its own colour
+# whilst being able to visually associate them back to their nextstrain clade.
+#
+# The order in the list must be hierarchical w.r.t pango lineages, i.e. XBB.1.9
+# must appear _before_ XBB
+#
+# NOTES:
+# * Lineages are ordered (in the legend & for the GA estimates) alphabetically
+#   via their full pango name. This doesn't map nicely onto nextstrain clade
+#   definitions, which is why an individual colour scale defined here may appear
+#   in multiple parts of the graph.
+# * Lineages which are not a descendant of a clade-defining lineage will be
+#   grouped as 'other'
+clade_definitions:
+  - clade: "24C"
+    display_name: "24C (KP.3)"
+    defining_lineage: "KP.3"
+    color: '#DC2F24'
+  - clade: "24B"
+    display_name: "24B (JN.1.11.1)"
+    defining_lineage: "JN.1.11.1"
+    color: '#E4632E'
+  - clade: "24A"
+    display_name: "24A (JN.1)"
+    defining_lineage: "JN.1"
+    color: '#E69136'
+  - clade: "23I"
+    display_name: "23I (BA.2.86)"
+    defining_lineage: "BA.2.86"
+    color: '#D9AD3D'
+  - clade: "23H"
+    display_name: "23H (HK.3)"
+    defining_lineage: "HK.3"
+    color: '#C1BA47'
+  - clade: "23G"
+    display_name: "23G (XBB.1.5.70)"
+    defining_lineage: "XBB.1.5.70"
+    color: '#A2BE57'
+  - clade: "23F"
+    display_name: "23F (EG.5.1)"
+    defining_lineage: "EG.5.1"
+    color: '#83BA70'
+  - clade: "23E"
+    display_name: "23E (XBB.2.3)"
+    defining_lineage: "XBB.2.3"
+    color: '#69B091'
+  - clade: "23D"
+    display_name: "23D (XBB.1.9)"
+    defining_lineage: "XBB.1.9"
+    color: '#549DB2'
+  - clade: "23C"
+    display_name: "23C (CH.1.1)"
+    defining_lineage: "CH.1.1"
+    color: '#4580CA'
+  - clade: "23B"
+    display_name: "23B (XBB.1.16)"
+    defining_lineage: "XBB.1.16"
+    color: '#3E58CF'
+  - clade: "22F"
+    display_name: "22F (XBB)"
+    defining_lineage: "XBB"
+    color: '#462EB9'
+  - clade: "other"
+    display_name: "other"
+    defining_lineage: False
+    color: '#777777'