WIP: SH tree

Author: j23414

phylogenetic/Snakefile

@@ -8,7 +8,7 @@ workdir: workflow.current_basedir
 # Use default configuration values. Override with Snakemake's --configfile/--config options.
 configfile: "defaults/config.yaml"
 
-builds = ["north-america","global"]
+builds = ["north-america","global","sh"]
 
 wildcard_constraints:
     build = "|".join(builds)

phylogenetic/defaults/color_orderings.tsv

@@ -298,11 +298,17 @@ MuV_genotype	A
 MuV_genotype	B
 MuV_genotype	C
 MuV_genotype	D
+MuV_genotype	D1
 MuV_genotype	F
 MuV_genotype	G
+MuV_genotype	G1
+MuV_genotype	G2
 MuV_genotype	H
+MuV_genotype	H1
+MuV_genotype	H2
 MuV_genotype	I
 MuV_genotype	J
 MuV_genotype	K
+MuV_genotype	K/M
 MuV_genotype	L
 MuV_genotype	N

phylogenetic/defaults/config.yaml

@@ -4,25 +4,30 @@ sequences_url: "https://data.nextstrain.org/files/workflows/mumps/sequences.fast
 metadata_url: "https://data.nextstrain.org/files/workflows/mumps/metadata.tsv.zst"
 
 strain_id_field: "accession"
-reference: "defaults/reference.gb"
+reference:
+  north-america: "defaults/reference.gb"
+  global: "defaults/reference.gb"
+  sh: "defaults/sh/reference.gb"
 
 filter:
-  min_length: 8000
   group_by: country year month MuV_genotype division
   specific:
-    north-america: --subsample-max-sequences 4000 --min-date 2006 --query "region=='North America' & (MuV_genotype=='G')"
-    global: --subsample-max-sequences 4000 --min-date 1950
+    north-america: --min-length 8000 --subsample-max-sequences 4000 --min-date 2006 --query "region=='North America' & (MuV_genotype=='G')"
+    global: --min-length 8000 --subsample-max-sequences 4000 --min-date 1950
+    sh: --exclude-all
 
 refine:
-  north-america: "--clock-filter-iqd 4"
-  global: ""
+  north-america: "--timetree --clock-filter-iqd 4 --coalescent opt --date-confidence --date-inference marginal"
+  global: "--timetree --coalescent opt --date-confidence --date-inference marginal"
+  sh: "--timetree --clock-rate 0.0001"
 
 ancestral:
   inference: "joint"
 
 traits:
   north-america: country division MuV_genotype
   global: region MuV_genotype
+  sh: region
   sampling_bias_correction: 3
 
 colors:

phylogenetic/defaults/sh/auspice_config.json

@@ -0,0 +1,96 @@
+{
+  "title": "Real-time tracking of mumps virus evolution",
+  "maintainers": [
+    {"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}
+  ],
+  "data_provenance": [
+    {
+      "name": "GenBank",
+      "url": "https://www.ncbi.nlm.nih.gov/genbank/"
+    }
+  ],
+  "build_url": "https://github.com/nextstrain/mumps",
+  "colorings": [
+    {
+      "key": "gt",
+      "title": "Genotype",
+      "type": "categorical"
+    },
+    {
+      "key": "num_date",
+      "title": "Date",
+      "type": "continuous"
+    },
+    {
+      "key": "author",
+      "title": "Author",
+      "type": "categorical"
+    },
+    {
+      "key": "MuV_genotype",
+      "title": "MuV genotype",
+      "type": "categorical"
+    },
+    {
+      "key": "country",
+      "title": "Country",
+      "type": "categorical"
+    },
+    {
+      "key": "region",
+      "title": "Region",
+      "type": "categorical"
+    },
+    {
+      "key": "duplicate",
+      "title": "Duplicate",
+      "type": "categorical"
+    }
+  ],
+  "geo_resolutions": [
+    "country",
+    "region"
+  ],
+  "panels": [
+    "tree",
+    "map",
+    "entropy",
+    "frequencies"
+  ],
+  "display_defaults": {
+    "map_triplicate": true,
+    "color_by": "country",
+    "tip_label": "strain"
+  },
+  "filters": [
+    "MuV_genotype",
+    "country",
+    "region",
+    "author"
+  ],
+  "metadata_columns": [
+    "strain",
+    "isolate",
+    "host",
+    "identical_to"
+  ],
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "MuV_genotype",
+          "displayName": "MuV Genotype",
+          "description": "Mumps genotype"
+        }
+      ],
+      "pathogen": {
+        "schemaVersion":"3.0.0",
+        "attributes": {
+          "name": "Mumps virus global tree",
+          "reference name": "Reconstructed ancestor from global tree",
+          "reference accession": "none"
+        }
+      }
+    }
+  }
+}