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}
  """