Fix phylo outbreak (#354)

* phylo: Update example data

Prompted by release of mpox Nextclade dataset that changed the values
in the `outbreak` column.

* phylo: Update `outbreak` filters in configs

Lates mpox Nextclade dataset updated the values in the `outbreak` such
that outbreak hMPXV-1 is now called sh2017.¹

Resolves #353

¹ <https://github.com/nextstrain/nextclade_data/releases/tag/2025-12-10--14-52-38Z>

* phylo: update hardcoded `hMPXV-1` values to `sh2017`

* Update changelog

Author: joverlee521

CHANGELOG.md

@@ -10,6 +10,9 @@ Instead, changes appear below grouped by the date they were added to the workflo
 
 ## 2025
 
+* 10 December 2025: BREAKING CHANGE - the `outbreak` column values have been updated with the latest release of the Nextclade dataset.
+  See [Nextclade release notes](https://github.com/nextstrain/nextclade_data/releases/tag/2025-12-10--14-52-38Z) for details.
+  * phylogenetic workflow's default filter params have been updated to replace outbreak `hMPXV-1` with `sh2017`
 * 10 November 2025: Transition to Pathoplexus as data source
   * Ingest workflow updated to pull data from Pathoplexus API instead of directly from INSDC databases.
   * Phylogenetic workflow updated to take into account changes in metadata and sequence data from Pathoplexus.

phylogenetic/build-configs/ci/config.yaml

@@ -34,7 +34,7 @@ subsample:
     --group-by lineage year country
     --sequences-per-group 50
     --exclude-where
-    outbreak!=hMPXV-1
+    outbreak!=sh2017
     clade!=IIb
     lineage=B.1
     lineage=B.1.1
@@ -85,7 +85,7 @@ subsample:
   b1: >-
     --group-by country year
     --subsample-max-sequences 300
-    --exclude-where outbreak!=hMPXV-1 clade!=IIb
+    --exclude-where outbreak!=sh2017 clade!=IIb
 
 ## align
 max_indel: 10000

phylogenetic/defaults/color_ordering.tsv

@@ -16894,7 +16894,7 @@ clade_membership	IIb
 
 ################
 
-outbreak	hMPXV-1
+outbreak	sh2017
 
 ################
 

phylogenetic/defaults/hmpxv1/config.yaml

@@ -34,7 +34,7 @@ subsample:
     --group-by lineage year country
     --sequences-per-group 75
     --exclude-where
-    outbreak!=hMPXV-1
+    outbreak!=sh2017
     clade!=IIb
     lineage=B.1
     lineage=B.1.1
@@ -86,7 +86,7 @@ subsample:
     --group-by country year
     --subsample-max-sequences 800
     --probabilistic-sampling
-    --exclude-where outbreak!=hMPXV-1 clade!=IIb
+    --exclude-where outbreak!=sh2017 clade!=IIb
 
 ## align
 max_indel: 10000

phylogenetic/defaults/hmpxv1_big/config.yaml

@@ -31,7 +31,7 @@ subsample:
     --group-by year month country
     --subsample-max-sequences 5000
     --exclude-where
-    outbreak!=hMPXV-1
+    outbreak!=sh2017
     clade!=IIb
     lineage=A
     lineage=A.1

phylogenetic/example_data/metadata.tsv

@@ -30,7 +30,7 @@
 
         # if it starts with clade -> it's a clade
         # if it starts with outbreak -> it's outbreak, need to look up clade
-        # if it starts with lineage -> it's clade IIb, outbreak hMPXV-1
+        # if it starts with lineage -> it's clade IIb, outbreak sh2017
         if old_clade_name.startswith("clade"):
             clade_name = old_clade_name.split()[1]
         # Need to set up clade dictionary for when we have other outbreaks
@@ -41,7 +41,7 @@
             clade_name = args.outgroup_clade_name
         else:
             clade_name = "IIb"
-            outbreak_name = "hMPXV-1"
+            outbreak_name = "sh2017"
             lineage_name = old_clade_name
 
         new_node_data[name] = {
@@ -52,7 +52,7 @@
         if "clade_annotation" in node:
             new_node_data[name]["clade_annotation"] = node["clade_annotation"]
             if node["clade_annotation"] == "A":
-                new_node_data[name]["clade_annotation"] = "hMPXV-1 A"
+                new_node_data[name]["clade_annotation"] = "sh2017 A"
 
     data["nodes"] = new_node_data
     with open(args.output_node_data, "w") as fh: