Merge pull request #1000 from nextstrain/new-augur-clades

Update workflow for new augur clades version

docs/src/reference/change_log.md

@@ -5,6 +5,10 @@ We also use this change log to document new features that maintain backward comp
 
 ## New features since last version update
 
+## v13 (16 May 2022)
+
+- 16 May 2023: Update workflow to support [Augur v22](https://github.com/nextstrain/augur/releases/tag/22.0.0) which updates the `augur clades` interface and structure of the output files to allow specifying the clade label & coloring keys. Because we use custom scripts to parse these files this worflow also needed updating. This change results in a simplifying of the nCoV pipeline (PR [1000](https://github.com/nextstrain/ncov/pull/1000)).
+
 - 11 April 2023: Elevate XBB.1.16 as new clade 23B. See [PR 1059](https://github.com/nextstrain/ncov/pull/1059) for the rationale behind this clade update.
 
 - 6 April 2023: Update conda environment dependencies: augur 19.2.0 -> 21.1.0, nextalign/nextclade 2.9.1 -> 2.13.1, iqtree 2.2.0_beta -> 2.2.0.3. [PR 1056](https://github.com/nextstrain/ncov/pull/1056)

workflow/envs/nextstrain.yaml

@@ -4,7 +4,7 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - augur=21.1.0
+  - augur=22.0.1
   - epiweeks=2.1.2
   - iqtree=2.2.0.3
   - nextalign=2.13.1

workflow/snakemake_rules/main_workflow.smk

@@ -1075,7 +1075,7 @@ rule emerging_lineages:
         emerging_lineages = config["files"]["emerging_lineages"],
         clades = config["files"]["clades"]
     output:
-        clade_data = "results/{build_name}/temp_emerging_lineages.json"
+        clade_data = "results/{build_name}/emerging_lineages.json"
     log:
         "logs/emerging_lineages_{build_name}.txt"
     benchmark:
@@ -1089,27 +1089,11 @@ rule emerging_lineages:
         augur clades --tree {input.tree} \
             --mutations {input.nuc_muts} {input.aa_muts} \
             --clades {input.emerging_lineages} \
+            --membership-name emerging_lineage \
+            --label-name emerging_lineage \
             --output-node-data {output.clade_data} 2>&1 | tee {log}
         """
 
-rule rename_emerging_lineages:
-    input:
-        node_data = rules.emerging_lineages.output.clade_data
-    output:
-        clade_data = "results/{build_name}/emerging_lineages.json"
-    benchmark:
-        "benchmarks/rename_emerging_lineages_{build_name}.txt"
-    run:
-        import json
-        with open(input.node_data, 'r', encoding='utf-8') as fh:
-            d = json.load(fh)
-            new_data = {}
-            for k,v in d['nodes'].items():
-                if "clade_membership" in v:
-                    new_data[k] = {"emerging_lineage": v["clade_membership"]}
-        with open(output.clade_data, "w") as fh:
-            json.dump({"nodes": new_data}, fh, indent=2)
-
 rule colors:
     message: "Constructing colors file"
     input:
@@ -1366,8 +1350,8 @@ def _get_node_data_by_wildcards(wildcards):
         rules.refine.output.node_data,
         rules.ancestral.output.node_data,
         rules.translate.output.node_data,
-        rules.rename_emerging_lineages.output.clade_data,
         rules.clades.output.clade_data,
+        rules.emerging_lineages.output.clade_data,
         rules.recency.output.node_data,
         rules.traits.output.node_data,
         rules.logistic_growth.output.node_data,
@@ -1462,28 +1446,10 @@ rule export:
             --output {output.auspice_json} 2>&1 | tee {log}
         """
 
-rule add_branch_labels:
-    message: "Adding custom branch labels to the Auspice JSON"
-    input:
-        auspice_json = rules.export.output.auspice_json,
-        emerging_clades = rules.emerging_lineages.output.clade_data
-    output:
-        auspice_json = "results/{build_name}/ncov_with_branch_labels.json"
-    log:
-        "logs/add_branch_labels{build_name}.txt"
-    conda: config["conda_environment"]
-    shell:
-        """
-        python3 ./scripts/add_branch_labels.py \
-            --input {input.auspice_json} \
-            --emerging-clades {input.emerging_clades} \
-            --output {output.auspice_json}
-        """
-
 rule include_hcov19_prefix:
     message: "Rename strains to include hCoV-19/ prefix"
     input:
-        auspice_json = rules.add_branch_labels.output.auspice_json,
+        auspice_json = rules.export.output.auspice_json,
         tip_frequencies = rules.tip_frequencies.output.tip_frequencies_json
     output:
         auspice_json = "results/{build_name}/ncov_with_hcov19_prefix.json",