phylo: add quality filters and clades to builds

nextstrain · Dec 13, 2023 · b260651 · b260651
1 parent 208c265
commit b260651
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Showing 4 changed files with 4 additions and 12 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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} \
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,9 +10,6 @@ It produces output files as @@
     """
-    TIME = ['1', '2','3']
     rule sort:
         input:
             sequences = rules.transform.output.sequences
@@ Expand Down @@