Merge pull request #1097 from nextstrain/remove-rbd

Remove RDB-level related rules/files
nextstrain · Feb 1, 2024 · 3bd4d42 · 3bd4d42
2 parents cec4fa0 + d359784
commit 3bd4d42
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Showing 6 changed files with 2 additions and 148 deletions.
diff --git a/defaults/parameters.yaml b/defaults/parameters.yaml
@@ -70,7 +70,6 @@ files:
   emerging_lineages: "defaults/emerging_lineages.tsv"
   mutational_fitness_distance_map: "defaults/mutational_fitness_distance_map.json"
   sites_to_mask: "defaults/sites_ignored_for_tree_topology.txt"
-  rbd_level_definitions: "defaults/rbd_levels.yaml"
 
 # Define genes to translate during alignment by nextalign.
 genes: ["ORF1a", "ORF1b", "S", "ORF3a", "E", "M", "ORF6", "ORF7a", "ORF7b", "ORF8", "N", "ORF9b"]

diff --git a/defaults/rbd_levels.yaml b/defaults/rbd_levels.yaml
diff --git a/docs/src/reference/change_log.md b/docs/src/reference/change_log.md
@@ -5,6 +5,8 @@ We also use this change log to document new features that maintain backward comp
 
 ## New features since last version update
 
+- 31 January 2024: Remove RBD-level related rules and files since this feature has been broken since May 2023 and is no longer relevant. [PR 1097](https://github.com/nextstrain/ncov/pull/1097)
+
 - 30 January 2024: Fix RBD-level coloring by updating clade label and clade parsing. [PR 1094](https://github.com/nextstrain/ncov/pull/1094)
 
 - 14 Dec 2023: Use `nextclade2` binary that makes the version explicit [PR 1089](https://github.com/nextstrain/ncov/pull/1089)

diff --git a/scripts/assign_rbd_levels.py b/scripts/assign_rbd_levels.py
diff --git a/workflow/snakemake_rules/export_for_nextstrain.smk b/workflow/snakemake_rules/export_for_nextstrain.smk
@@ -202,11 +202,6 @@ rule auspice_config:
                     "title": "S1 Mutations",
                     "type": "continuous"
                 },
-                {
-                    "key": "rbd_level",
-                    "title": "RBD Level",
-                    "type": "ordinal"
-                },
                 {
                     "key": "immune_escape",
                     "title": "Immune Escape vs BA.2",
@@ -311,7 +306,6 @@ rule auspice_config:
                 originating_lab_filter,
                 submitting_lab_filter,
                 "recency",
-                "rbd_level",
             ],
             "panels": [
                 "tree",

diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk
@@ -1297,32 +1297,6 @@ rule find_clusters:
            --output {output.clusters}
        """
 
-rule assign_rbd_levels:
-    input:
-        spike_alignment="results/{build_name}/translations/aligned.gene.S_withInternalNodes.fasta",
-        clades="results/{build_name}/clades.json",
-        tree = "results/{build_name}/tree.nwk",
-    params:
-        config=config["files"]["rbd_level_definitions"],
-        basal_clade_label="21L (BA.2)"
-    output:
-        node_data="results/{build_name}/rbd_levels.json",
-    log:
-        "logs/assign_rbd_levels_{build_name}.txt"
-    benchmark:
-        "benchmarks/assign_rbd_levels_{build_name}.txt",
-    conda:
-        config["conda_environment"],
-    shell:
-        """
-        python3 scripts/assign_rbd_levels.py \
-            --spike-alignment {input.spike_alignment} \
-            --config {params.config} \
-            --clades-node-data {input.clades} \
-            --basal-clade-label {params.basal_clade_label:q} \
-            --tree {input.tree} \
-            --output-node-data {output.node_data} 2>&1 | tee {log}
-        """
 
 def export_title(wildcards):
     # TODO: maybe we could replace this with a config entry for full/human-readable build name?
@@ -1360,7 +1334,6 @@ def _get_node_data_by_wildcards(wildcards):
         rules.mutational_fitness.output.node_data,
         rules.distances.output.node_data,
         rules.calculate_epiweeks.output.node_data,
-        rules.assign_rbd_levels.output.node_data,
     ]
 
     if "run_pangolin" in config and config["run_pangolin"]: