From b260651b278a73fc9b507427aec009a95fe85932 Mon Sep 17 00:00:00 2001
From: Richard Neher <richard.neher@unibas.ch>
Date: Wed, 13 Dec 2023 18:01:57 +0100
Subject: [PATCH] phylo: add quality filters and clades to builds

---
 config/auspice_config.json               | 5 -----
 ingest/workflow/snakemake_rules/sort.smk | 3 ---
 workflow/snakemake_rules/core.smk        | 1 +
 workflow/snakemake_rules/export.smk      | 7 +++----
 4 files changed, 4 insertions(+), 12 deletions(-)

diff --git a/config/auspice_config.json b/config/auspice_config.json
index c349466..82cba3f 100644
--- a/config/auspice_config.json
+++ b/config/auspice_config.json
@@ -14,11 +14,6 @@
   "build_url": "https://github.com/nextstrain/rsv",
 
   "colorings": [
-    {
-      "key": "genome_clade",
-      "title": "Genome Clade",
-      "type": "categorical"
-    },
     {
       "key": "gt",
       "title": "Genotype",
diff --git a/ingest/workflow/snakemake_rules/sort.smk b/ingest/workflow/snakemake_rules/sort.smk
index 331b1d9..1eaf6a3 100644
--- a/ingest/workflow/snakemake_rules/sort.smk
+++ b/ingest/workflow/snakemake_rules/sort.smk
@@ -10,9 +10,6 @@ It produces output files as
 
 """
 
-TIME = ['1', '2','3']
-
-
 rule sort:
     input:
         sequences = rules.transform.output.sequences
diff --git a/workflow/snakemake_rules/core.smk b/workflow/snakemake_rules/core.smk
index c323962..e87b63e 100644
--- a/workflow/snakemake_rules/core.smk
+++ b/workflow/snakemake_rules/core.smk
@@ -68,6 +68,7 @@ rule filter:
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
             --exclude {input.exclude} \
+            --exclude-where 'qc.overallStatus=bad' \
             --output {output.sequences} \
             --group-by {params.group_by} \
             --subsample-max-sequences {params.subsample_max_sequences} \
diff --git a/workflow/snakemake_rules/export.smk b/workflow/snakemake_rules/export.smk
index b1b713b..6d8e9ec 100644
--- a/workflow/snakemake_rules/export.smk
+++ b/workflow/snakemake_rules/export.smk
@@ -6,10 +6,8 @@ def get_node_data(w):
     if w.build_name in config["genesforglycosylation"]:
         node_data.append(rules.glycosylation.output.glycosylations)
     if w.build_name == "genome":
-        node_data.append(rules.clades_genome.output.node_data)
         node_data.append(rules.clades_consortium.output.node_data)
-    if w.build_name in ["genome", "G"]:
-        node_data.append(rules.clades_Goya.output.node_data)
+
     return node_data
 
 rule colors:
@@ -43,11 +41,12 @@ rule export:
     params:
     	title = lambda w: f"RSV-{w.a_or_b.upper()} phylogeny",
         strain_id=config["strain_id_field"],
+        metadata_colors = lambda w: '' if w.build_name=='genome' else f"--color-by-metadata clade"
     shell:
         """
         augur export v2 \
             --tree {input.tree} \
-            --metadata {input.metadata} \
+            --metadata {input.metadata} {params.metadata_colors} \
             --metadata-id-columns {params.strain_id} \
             --node-data {input.node_data} \
             --title {params.title:q} \