From 388c15a2cb56d8c3831602d42ada762611d1605d Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Fri, 22 Nov 2024 09:43:13 -0800
Subject: [PATCH] Link out to Nextclade (#49)

* Add root sequence to the exported auspice json files
* Add 'lineage' to traits inference
* Add 'lineage' to global auspice config
* Add descriptive names for each of the Nextclade datasets
---
 .../washington-state-rules.smk                |  1 +
 phylogenetic/defaults/auspice_config.json     | 15 ++++++++++++-
 .../defaults/auspice_config_global.json       | 22 ++++++++++++++++++-
 phylogenetic/defaults/config.yaml             |  3 ++-
 phylogenetic/rules/export.smk                 |  1 +
 5 files changed, 39 insertions(+), 3 deletions(-)

diff --git a/phylogenetic/build-configs/washington-state/washington-state-rules.smk b/phylogenetic/build-configs/washington-state/washington-state-rules.smk
index f2a1c77..2c1af88 100644
--- a/phylogenetic/build-configs/washington-state/washington-state-rules.smk
+++ b/phylogenetic/build-configs/washington-state/washington-state-rules.smk
@@ -69,6 +69,7 @@ rule export_washington_build:
             --lat-longs {input.lat_longs} \
             --description {input.description} \
             --auspice-config {input.auspice_config} \
+            --include-root-sequence-inline \
             --output {output.auspice} 2>&1 | tee {log}
         """
 
diff --git a/phylogenetic/defaults/auspice_config.json b/phylogenetic/defaults/auspice_config.json
index 3913356..722a17c 100644
--- a/phylogenetic/defaults/auspice_config.json
+++ b/phylogenetic/defaults/auspice_config.json
@@ -46,5 +46,18 @@
     "map_triplicate": true,
     "geo_resolution": "state",
     "distance_measure": "div"
- }
+  },
+  "extensions": {
+    "nextclade": {
+      "pathogen": {
+        "schemaVersion":"3.0.0",
+        "defaultCds": "env",
+        "attributes": {
+          "name": "West Nile Virus Washington-State-Focused Tree",
+          "reference name": "IS88",
+          "reference accession": "AF481864"
+        }
+      }
+    }
+  }
 }
diff --git a/phylogenetic/defaults/auspice_config_global.json b/phylogenetic/defaults/auspice_config_global.json
index b7b598b..5a1ad86 100644
--- a/phylogenetic/defaults/auspice_config_global.json
+++ b/phylogenetic/defaults/auspice_config_global.json
@@ -39,5 +39,25 @@
     "color_by": "region",
     "map_triplicate": true,
     "geo_resolution": "country"
- }
+ },
+  "extensions": {
+    "nextclade": {
+      "clade_node_attrs": [
+        {
+          "name": "lineage",
+          "displayName": "Pathoplexus lineage",
+          "description": "Global WNV lineages based on pathoplexus results."
+        }
+      ],
+      "pathogen": {
+        "schemaVersion":"3.0.0",
+        "defaultCds": "env",
+        "attributes": {
+          "name": "West Nile Virus Global Tree",
+          "reference name": "Reconstructed ancestor from global tree",
+          "reference accession": "none"
+        }
+      }
+    }
+  }
 }
diff --git a/phylogenetic/defaults/config.yaml b/phylogenetic/defaults/config.yaml
index ef9c5c5..ef02a85 100644
--- a/phylogenetic/defaults/config.yaml
+++ b/phylogenetic/defaults/config.yaml
@@ -74,7 +74,8 @@ refine:
 traits:
   metadata_columns: [
     'region',
-    'country'
+    'country',
+    'lineage',
   ]
 
 export:
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
index 41b89d0..d1953b7 100644
--- a/phylogenetic/rules/export.smk
+++ b/phylogenetic/rules/export.smk
@@ -51,5 +51,6 @@ rule export:
             --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} \
             --description {input.description} \
             --auspice-config {input.auspice_config} \
+            --include-root-sequence-inline \
             --output {output.auspice} 2>&1 | tee {log}
         """