Merge pull request #166 from nextstrain/inline-root

inline root sequence
nextstrain · May 30, 2024 · 2d0f3d0 · 2d0f3d0
2 parents 08d2c1b + 4431664
commit 2d0f3d0
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Showing 5 changed files with 6 additions and 29 deletions.
diff --git a/Snakefile b/Snakefile
@@ -71,7 +71,6 @@ def _get_build_outputs():
         for segment in config["segments"]:
             outputs.extend([
                 f"auspice/{build_name}_{segment}.json",
-                f"auspice/{build_name}_{segment}_root-sequence.json",
                 f"auspice/{build_name}_{segment}_tip-frequencies.json",
             ])
 

diff --git a/profiles/nextflu-private-forecasts/rename.smk b/profiles/nextflu-private-forecasts/rename.smk
@@ -5,7 +5,7 @@ rule all_public:
             "auspice_renamed/" + build.get("auspice_name", f"{build_name}_{{segment}}").format(segment=segment) + suffix + ".json"
             for build_name, build in config["builds"].items()
             for segment in config["segments"]
-            for suffix in ["", "_root-sequence", "_tip-frequencies", "_measurements"]
+            for suffix in ["", "_tip-frequencies", "_measurements"]
         ],
 
 def _get_file_by_auspice_name(wildcards):
@@ -26,16 +26,6 @@ rule rename_auspice_main:
         ln {input} {output}
         """
 
-rule rename_auspice_root_sequence:
-    input:
-        lambda wildcards: _get_file_by_auspice_name(wildcards).replace(".json", "_root-sequence.json"),
-    output:
-        "auspice_renamed/{auspice_name}_root-sequence.json",
-    shell:
-        """
-        ln {input} {output}
-        """
-
 rule rename_auspice_tip_frequencies:
     input:
         lambda wildcards: _get_file_by_auspice_name(wildcards).replace(".json", "_tip-frequencies.json"),

diff --git a/profiles/nextflu-private/antigenic_distances.smk b/profiles/nextflu-private/antigenic_distances.smk
@@ -174,8 +174,7 @@ rule export_private:
         auspice_config = lambda w: config['builds'][w.build_name]['auspice_config'],
         lat_longs = config['lat-longs']
     output:
-        auspice_json = "auspice/{build_name}_{segment}.json",
-        root_sequence_json = "auspice/{build_name}_{segment}_root-sequence.json",
+        auspice_json = "auspice/{build_name}_{segment}.json"
     conda: "../../workflow/envs/nextstrain.yaml"
     benchmark:
         "benchmarks/export_{build_name}_{segment}.txt"
@@ -187,7 +186,7 @@ rule export_private:
             --tree {input.tree} \
             --metadata {input.metadata} \
             --node-data {input.node_data} {input.private_node_data} \
-            --include-root-sequence \
+            --include-root-sequence-inline \
             --lat-longs {input.lat_longs} \
             --auspice-config {input.auspice_config} \
             --minify-json \

diff --git a/profiles/nextstrain-public/rename.smk b/profiles/nextstrain-public/rename.smk
@@ -5,7 +5,7 @@ rule all_public:
             "auspice_renamed/" + build.get("auspice_name", f"{build_name}_{{segment}}").format(segment=segment) + suffix + ".json"
             for build_name, build in config["builds"].items()
             for segment in config["segments"]
-            for suffix in ["", "_root-sequence", "_tip-frequencies"]
+            for suffix in ["", "_tip-frequencies"]
         ],
 
 def _get_file_by_auspice_name(wildcards):
@@ -26,16 +26,6 @@ rule rename_auspice_main:
         ln {input} {output}
         """
 
-rule rename_auspice_root_sequence:
-    input:
-        lambda wildcards: _get_file_by_auspice_name(wildcards).replace(".json", "_root-sequence.json"),
-    output:
-        "auspice_renamed/{auspice_name}_root-sequence.json",
-    shell:
-        """
-        ln {input} {output}
-        """
-
 rule rename_auspice_tip_frequencies:
     input:
         lambda wildcards: _get_file_by_auspice_name(wildcards).replace(".json", "_tip-frequencies.json"),

diff --git a/workflow/snakemake_rules/export.smk b/workflow/snakemake_rules/export.smk
@@ -61,8 +61,7 @@ rule export:
         auspice_config = lambda w: config['builds'][w.build_name]['auspice_config'],
         lat_longs = config.get('lat-longs', "config/lat_longs.tsv"),
     output:
-        auspice_json = "auspice/{build_name}_{segment}.json",
-        root_sequence_json = "auspice/{build_name}_{segment}_root-sequence.json",
+        auspice_json = "auspice/{build_name}_{segment}.json"
     conda: "../envs/nextstrain.yaml"
     benchmark:
         "benchmarks/export_{build_name}_{segment}.txt"
@@ -74,7 +73,7 @@ rule export:
             --tree {input.tree} \
             --metadata {input.metadata} \
             --node-data {input.node_data} \
-            --include-root-sequence \
+            --include-root-sequence-inline \
             --lat-longs {input.lat_longs} \
             --auspice-config {input.auspice_config} \
             --output {output.auspice_json} 2>&1 | tee {log}