From 4051dc0ab2ce0179829bcf47ab3b5350b3055615 Mon Sep 17 00:00:00 2001
From: Kim Andrews <17375001+kimandrews@users.noreply.github.com>
Date: Tue, 28 May 2024 13:25:24 -0700
Subject: [PATCH] Remove time information from Nextclade dataset tree

Removes temporal info from Nextclade dataset timetree, since Nextclade doesn't use this information. This change was recommended here: https://github.com/nextstrain/nextclade_data/pull/202#issuecomment-2130148472
---
 nextclade/defaults/auspice_config.json  | 5 -----
 nextclade/rules/construct_phylogeny.smk | 2 --
 nextclade/rules/export.smk              | 3 +--
 3 files changed, 1 insertion(+), 9 deletions(-)

diff --git a/nextclade/defaults/auspice_config.json b/nextclade/defaults/auspice_config.json
index 07109d8..9f6c685 100644
--- a/nextclade/defaults/auspice_config.json
+++ b/nextclade/defaults/auspice_config.json
@@ -11,11 +11,6 @@
       "title": "Genotype",
       "type": "categorical"
     },
-    {
-      "key": "num_date",
-      "title": "Date",
-      "type": "continuous"
-    },
     {
       "key": "clade_membership",
       "title": "MeV Genotype (Nextstrain)",
diff --git a/nextclade/rules/construct_phylogeny.smk b/nextclade/rules/construct_phylogeny.smk
index 5a34b9e..45a1554 100644
--- a/nextclade/rules/construct_phylogeny.smk
+++ b/nextclade/rules/construct_phylogeny.smk
@@ -31,7 +31,6 @@ rule refine:
         metadata = "data/metadata.tsv"
     output:
         tree = "results/tree.nwk",
-        node_data = "results/branch_lengths.json"
     params:
         coalescent = config["refine"]["coalescent"],
         date_inference = config["refine"]["date_inference"],
@@ -45,7 +44,6 @@ rule refine:
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
             --output-tree {output.tree} \
-            --output-node-data {output.node_data} \
             --timetree \
             --coalescent {params.coalescent} \
             --date-confidence \
diff --git a/nextclade/rules/export.smk b/nextclade/rules/export.smk
index 45ac446..894622a 100644
--- a/nextclade/rules/export.smk
+++ b/nextclade/rules/export.smk
@@ -10,7 +10,6 @@ rule export:
     input:
         tree = "results/tree.nwk",
         metadata = "data/metadata.tsv",
-        branch_lengths = "results/branch_lengths.json",
         clades = "results/clades.json",
         nt_muts = "results/nt_muts.json",
         aa_muts = "results/aa_muts.json",
@@ -27,7 +26,7 @@ rule export:
             --tree {input.tree} \
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
-            --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} {input.clades} \
+            --node-data {input.nt_muts} {input.aa_muts} {input.clades} \
             --colors {input.colors} \
             --metadata-columns {params.metadata_columns} \
             --auspice-config {input.auspice_config} \