Merge pull request #61 from nextstrain/feat/nextclade_compatibility

inline root sequence, add pathogen json and nextclade extension

Snakefile

@@ -1,5 +1,8 @@
 configfile: "config/configfile.yaml"
 
+wildcard_constraints:
+    a_or_b = r"a|b"
+
 build_dir = 'results'
 auspice_dir = 'auspice'
 
@@ -8,9 +11,6 @@ rule all:
         expand("auspice/rsv_{subtype}_{build}.json",
                subtype = config.get("subtypes",['a']),
                build = config.get("buildstorun", ['genome'])),
-        expand("auspice/rsv_{subtype}_{build}_root-sequence.json",
-               subtype = config.get("subtypes",['a']),
-               build = config.get("buildstorun", ['genome']))
 
 include: "workflow/snakemake_rules/chores.smk"
 

config/configfile.yaml

@@ -38,4 +38,14 @@ ancestral:
   inference: "joint"
 
 traits:
-  columns: "country"
+  columns: "country"
+
+nextclade_attributes:
+  a:
+    name: "RSV-A NextClade using real-time tree"
+    reference_name: "hRSV/A/England/397/2017"
+    accession: "EPI_ISL_412866"
+  b:
+    name: "RSV-B NextClade using real-time tree"
+    reference_name: "hRSV/B/Australia/VIC-RCH056/2019"
+    accession: "EPI_ISL_1653999"

nextclade/Snakefile

@@ -330,6 +330,7 @@ rule export:
             --node-data {input.node_data}\
             --auspice-config {input.auspice_config} \
             --color-by-metadata {params.fields} \
+            --include-root-sequence-inline \
             --minify-json \
             --title "Nextclade reference tree for RSV-{wildcards.a_or_b} with root {wildcards.reference} built on {params.date}" \
             --output {output.auspice_json} 2>&1;

scripts/clade_names.py → scripts/rename_and_nextclade.py

@@ -17,15 +17,30 @@ def replace_clade_recursive(node):
     )
 
     parser.add_argument('--input-auspice-json', type=str, required=True, help="input auspice_json")
+    parser.add_argument('--pathogen-json', type=str, required=True, help="pathogen json")
+    parser.add_argument('--reference', type=str, required=True, help="reference")
+    parser.add_argument('--build-name', type=str, required=True, help="nextclade build name")
+    parser.add_argument('--reference-accession', type=str, required=True, help="reference accession")
     parser.add_argument('--output', type=str, metavar="JSON", required=True, help="output Auspice JSON")
     args = parser.parse_args()
 
+    # read pathogen json
+    with open(args.pathogen_json, 'r') as fh:
+        pathogen_data = json.load(fh)
+
     with open(args.input_auspice_json, 'r') as fh:
         data = json.load(fh)
 
     data["meta"]["colorings"] = [x for x in data["meta"]["colorings"]
                                  if x["key"] != "genome_clade_annotation"]
     replace_clade_recursive(data['tree'])
 
+    # remove unneeded files structure
+    pathogen_data.pop("files")
+
+    pathogen_data["attributes"] = {"reference accession": args.reference_accession, "reference name": args.reference, "name": args.build_name}
+    pathogen_data["experimental"] = True
+    data["meta"]["extensions"] = {'nextclade': {'pathogen': pathogen_data}}
+
     with open(args.output, 'w') as fh:
         json.dump(data, fh, indent=0)

workflow/snakemake_rules/core.smk

@@ -213,7 +213,8 @@ rule ancestral:
         """
     input:
         tree = rules.refine.output.tree,
-        alignment = get_alignment
+        alignment = get_alignment,
+        root_sequence = build_dir + "/{a_or_b}/{build_name}/{build_name}_reference.gbk"
     output:
         node_data = build_dir + "/{a_or_b}/{build_name}/nt_muts.json"
     params:
@@ -224,6 +225,7 @@ rule ancestral:
             --tree {input.tree} \
             --alignment {input.alignment} \
             --output-node-data {output.node_data} \
+            --root-sequence {input.root_sequence} \
             --inference {params.inference}
         """
 

workflow/snakemake_rules/export.smk

@@ -36,8 +36,7 @@ rule export:
         auspice_config = config["files"]["auspice_config"],
         description = config["description"]
     output:
-        auspice_json =  build_dir + "/{a_or_b}/{build_name}/tree.json",
-        root_sequence = build_dir + "/{a_or_b}/{build_name}/tree_root-sequence.json"
+        auspice_json =  build_dir + "/{a_or_b}/{build_name}/tree.json"
     params:
         title = lambda w: f"RSV-{w.a_or_b.upper()} phylogeny",
         strain_id=config["strain_id_field"],
@@ -53,7 +52,7 @@ rule export:
             --description {input.description} \
             --colors {input.colors} \
             --auspice-config {input.auspice_config} \
-            --include-root-sequence \
+            --include-root-sequence-inline \
             --output {output.auspice_json}
         """
 
@@ -76,18 +75,23 @@ rule final_strain_name:
         """
 
 
-rule rename_clade_labels:
+rule rename_and_ready_for_nextclade:
     input:
         auspice_json= rules.final_strain_name.output.auspice_json,
-        root_sequence= rules.export.output.root_sequence
+        pathogen_json= "nextclade/config/pathogen.json"
     output:
-        auspice_json= "auspice/rsv_{a_or_b}_{build_name}.json",
-        root_sequence= "auspice/rsv_{a_or_b}_{build_name}_root-sequence.json"
+        auspice_json= "auspice/rsv_{a_or_b}_{build_name}.json"
+    params:
+        accession= lambda w: config["nextclade_attributes"][w.a_or_b]["accession"],
+        name= lambda w: config["nextclade_attributes"][w.a_or_b]["name"],
+        ref_name= lambda w: config["nextclade_attributes"][w.a_or_b]["reference_name"]
     shell:
         """
-        python3 scripts/clade_names.py  \
+        python3 scripts/rename_and_nextclade.py  \
                 --input-auspice-json {input.auspice_json} \
+                --pathogen-json {input.pathogen_json} \
+                --reference {params.ref_name:q} \
+                --build-name {params.name:q} \
+                --reference-accession {params.accession:q} \
                 --output {output.auspice_json}
-
-        cp {input.root_sequence} {output.root_sequence}
         """