Merge pull request #181 from nextstrain/add-emerging-clades

Add emerging subclades to nextflu-private builds
nextstrain · Sep 16, 2024 · 2489228 · 2489228
2 parents bddf3d1 + c23d20d
commit 2489228
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diff --git a/Snakefile b/Snakefile
@@ -48,6 +48,21 @@ subclade_url_by_lineage_and_segment = {
     }
 }
 
+emerging_subclade_url_by_lineage_and_segment = {
+    "h1n1pdm": {
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/main/.auto-generated/subclades.tsv",
+        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_NA/main/.auto-generated/subclades.tsv",
+    },
+    "h3n2": {
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/emerging/.auto-generated/subclades.tsv",
+        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/main/.auto-generated/subclades.tsv",
+    },
+    "vic": {
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_B-Vic_HA/main/.auto-generated/subclades.tsv",
+        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_B-Vic_NA/main/.auto-generated/subclades.tsv",
+    }
+}
+
 if "data_source" in config and config["data_source"]=='fauna':
     include: "workflow/snakemake_rules/download_from_fauna.smk"
 

diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json
@@ -75,6 +75,45 @@
         ]
       ]
     },
+    {
+      "key": "emerging_subclade",
+      "title": "Emerging subclade",
+      "type": "categorical",
+      "scale": [
+        [
+          "J",
+          "#4068CF"
+        ],
+        [
+          "J.1",
+          "#5098B9"
+        ],
+        [
+          "J.1.1",
+          "#6CB28C"
+        ],
+        [
+          "J.2",
+          "#94BD62"
+        ],
+        [
+          "J.2.1",
+          "#BFBB47"
+        ],
+        [
+          "J.2.2",
+          "#DFA53B"
+        ],
+        [
+          "J.3",
+          "#E67131"
+        ],
+        [
+          "J.4",
+          "#DB2823"
+        ]
+      ]
+    },
     {
       "key": "haplotype",
       "title": "Derived haplotype",

diff --git a/nextclade/config/config_dict.yaml b/nextclade/config/config_dict.yaml
@@ -51,6 +51,9 @@ builds:
         short-clade:
           url: "seasonal_A-H3N2_HA/main/.auto-generated/clades.tsv"
           key: "short-clade"
+        emerging_subclade:
+          url: "seasonal_A-H3N2_HA/emerging/.auto-generated/subclades.tsv"
+          key: "emerging_subclade"
       refs:
         EPI1857216:
           filter: "--min-date 2019 --probabilistic-sampling --group-by year region --min-length 1500 --subsample-max-sequences 2000"

diff --git a/profiles/nextflu-private-forecasts.yaml b/profiles/nextflu-private-forecasts.yaml
@@ -57,6 +57,7 @@ array-builds:
       tree_exclude_sites: "config/h3n2/{{segment}}/exclude-sites.txt"
       clades: "config/h3n2/ha/clades.tsv"
       subclades: "config/h3n2/ha/subclades.tsv"
+      emerging_subclades: "config/h3n2/ha/emerging_subclades.tsv"
       auspice_config: "profiles/nextflu-private/h3n2/ha/auspice_config.json"
       vaccines: "config/h3n2/vaccine.json"
       enable_titer_models: true

diff --git a/profiles/nextflu-private.yaml b/profiles/nextflu-private.yaml
@@ -56,6 +56,7 @@ builds:
     tree_exclude_sites: "config/h1n1pdm/{segment}/exclude-sites.txt"
     clades: "config/h1n1pdm/ha/clades.tsv"
     subclades: "config/h1n1pdm/{segment}/subclades.tsv"
+    emerging_subclades: "config/h1n1pdm/{segment}/emerging_subclades.tsv"
     auspice_config: "profiles/nextflu-private/h1n1pdm/{segment}/auspice_config.json"
     min_date: "2Y"
     reference_min_date: "6Y"
@@ -104,6 +105,7 @@ builds:
     tree_exclude_sites: "config/h3n2/{segment}/exclude-sites.txt"
     clades: "config/h3n2/ha/clades.tsv"
     subclades: "config/h3n2/{segment}/subclades.tsv"
+    emerging_subclades: "config/h3n2/{segment}/emerging_subclades.tsv"
     auspice_config: "profiles/nextflu-private/h3n2/{segment}/auspice_config.json"
     vaccines: "config/h3n2/vaccine.json"
     enable_glycosylation: true
@@ -149,6 +151,7 @@ builds:
     tree_exclude_sites: "config/vic/{segment}/exclude-sites.txt"
     clades: "profiles/nextflu-private/vic/ha/clades.tsv"
     subclades: "config/vic/{segment}/subclades.tsv"
+    emerging_subclades: "config/h3n2/{segment}/emerging_subclades.tsv"
     auspice_config: "profiles/nextflu-private/vic/{segment}/auspice_config.json"
     min_date: "2Y"
     reference_min_date: "6Y"

diff --git a/profiles/nextflu-private/h1n1pdm/ha/auspice_config.json b/profiles/nextflu-private/h1n1pdm/ha/auspice_config.json
@@ -129,6 +129,69 @@
         ]
       ]
     },
+    {
+      "key": "emerging_subclade",
+      "title": "Emerging subclade",
+      "type": "categorical",
+      "scale": [
+        [
+          "C.1",
+          "#492AB5"
+        ],
+        [
+          "C.1.1",
+          "#3F4CCB"
+        ],
+        [
+          "C.1.2",
+          "#4271CE"
+        ],
+        [
+          "C.1.5",
+          "#4C8FC0"
+        ],
+        [
+          "C.1.7",
+          "#5AA5A8"
+        ],
+        [
+          "C.1.7.1",
+          "#6DB38A"
+        ],
+        [
+          "C.1.7.2",
+          "#85BA6F"
+        ],
+        [
+          "C.1.8",
+          "#A0BE59"
+        ],
+        [
+          "C.1.9",
+          "#BBBC49"
+        ],
+        [
+          "D",
+          "#D2B340"
+        ],
+        [
+          "D.1",
+          "#E19F3A"
+        ],
+        [
+          "D.2",
+          "#E68033"
+        ],
+        [
+          "D.3",
+          "#E2562B"
+        ],
+        [
+          "D.4",
+          "#DB2823"
+        ]
+      ]
+    },
     {
       "key": "haplotype",
       "title": "Derived haplotype",

diff --git a/profiles/nextflu-private/h3n2/ha/auspice_config.json b/profiles/nextflu-private/h3n2/ha/auspice_config.json
@@ -141,6 +141,45 @@
         ]
       ]
     },
+    {
+      "key": "emerging_subclade",
+      "title": "Emerging subclade",
+      "type": "categorical",
+      "scale": [
+        [
+          "J",
+          "#4068CF"
+        ],
+        [
+          "J.1",
+          "#5098B9"
+        ],
+        [
+          "J.1.1",
+          "#6CB28C"
+        ],
+        [
+          "J.2",
+          "#94BD62"
+        ],
+        [
+          "J.2.1",
+          "#BFBB47"
+        ],
+        [
+          "J.2.2",
+          "#DFA53B"
+        ],
+        [
+          "J.3",
+          "#E67131"
+        ],
+        [
+          "J.4",
+          "#DB2823"
+        ]
+      ]
+    },
     {
       "key": "haplotype",
       "title": "Derived haplotype",
@@ -555,4 +594,4 @@
     "entropy",
     "frequencies"
   ]
-}
+}
diff --git a/profiles/nextflu-private/vic/ha/auspice_config.json b/profiles/nextflu-private/vic/ha/auspice_config.json
@@ -79,6 +79,41 @@
         ]
       ]
     },
+    {
+      "key": "emerging_subclade",
+      "title": "Emerging subclade",
+      "type": "categorical",
+      "scale": [
+        [
+          "C.2",
+          "#4272CE"
+        ],
+        [
+          "C.3",
+          "#58A2AC"
+        ],
+        [
+          "C.5",
+          "#7DB877"
+        ],
+        [
+          "C.5.1",
+          "#AEBD50"
+        ],
+        [
+          "C.5.4",
+          "#D8AE3E"
+        ],
+        [
+          "C.5.6",
+          "#E67A32"
+        ],
+        [
+          "C.5.7",
+          "#DB2823"
+        ]
+      ]
+    },
     {
       "key": "haplotype",
       "title": "Derived haplotype",

diff --git a/profiles/nextstrain-public.yaml b/profiles/nextstrain-public.yaml
@@ -205,6 +205,7 @@ array-builds:
       tree_exclude_sites: "config/{lineage}/{{segment}}/exclude-sites.txt"
       clades: "config/{lineage}/ha/clades.tsv"
       subclades: "config/{lineage}/{{segment}}/subclades.tsv"
+      emerging_subclades: "config/h3n2/{{segment}}/emerging_subclades.tsv"
       auspice_config: "config/{lineage}/{{segment}}/auspice_config.json"
       vaccines: "config/{lineage}/vaccine.json"
       enable_glycosylation: true

diff --git a/workflow/snakemake_rules/core.smk b/workflow/snakemake_rules/core.smk
@@ -420,6 +420,43 @@ rule import_clades:
             --output {output.node_data} 2>&1 | tee {log}
         """
 
+rule download_emerging_subclades:
+    output:
+        subclades="config/{lineage}/{segment}/emerging_subclades.tsv",
+    conda: "../envs/nextstrain.yaml"
+    params:
+        url=lambda wildcards: emerging_subclade_url_by_lineage_and_segment.get(wildcards.lineage, {}).get(wildcards.segment),
+    shell:
+        """
+        curl -o {output.subclades} "{params.url}"
+        """
+
+rule emerging_subclades:
+    input:
+        tree = build_dir + "/{build_name}/{segment}/tree.nwk",
+        muts = build_dir + "/{build_name}/{segment}/muts.json",
+        clades = lambda wildcards: config["builds"][wildcards.build_name].get("emerging_subclades"),
+    output:
+        node_data = build_dir + "/{build_name}/{segment}/emerging_subclades.json",
+    params:
+        membership_name = "emerging_subclade",
+        label_name = "Emerging subclade",
+    conda: "../envs/nextstrain.yaml"
+    benchmark:
+        "benchmarks/emerging_subclades_{build_name}_{segment}.txt"
+    log:
+        "logs/emerging_subclades_{build_name}_{segment}.txt"
+    shell:
+        """
+        augur clades \
+            --tree {input.tree} \
+            --mutations {input.muts} \
+            --clades {input.clades} \
+            --membership-name {params.membership_name} \
+            --label-name {params.label_name:q} \
+            --output {output.node_data} 2>&1 | tee {log}
+        """
+
 rule annotate_haplotypes:
     input:
         tree=build_dir + "/{build_name}/ha/tree.nwk",

diff --git a/workflow/snakemake_rules/export.smk b/workflow/snakemake_rules/export.smk
@@ -23,6 +23,9 @@ def _get_node_data_by_wildcards(wildcards):
     if config["builds"][wildcards.build_name].get('subclades', False):
         inputs.append(rules.subclades.output.node_data)
 
+    if config["builds"][wildcards.build_name].get('emerging_subclades', False):
+        inputs.append(rules.emerging_subclades.output.node_data)
+
     if config["builds"][wildcards.build_name].get('enable_titer_models', False) and wildcards.segment == 'ha':
         for collection in config["builds"][wildcards.build_name]["titer_collections"]:
             inputs.append(rules.titers_sub.output.titers_model.format(titer_collection=collection["name"], **wildcards_dict))

diff --git a/workflow/snakemake_rules/fitness.smk b/workflow/snakemake_rules/fitness.smk
@@ -380,6 +380,8 @@ rule forecast_tips:
         "benchmarks/forecast_tips_{build_name}_{segment}_{model}.txt"
     log:
         "logs/forecast_tips_{build_name}_{segment}_{model}.txt"
+    resources:
+        mem_mb=8000,
     shell:
         """
         python3 flu-forecasting/src/forecast_model.py \