inline root sequence

nextstrain · May 30, 2024 · e20ad52 · e20ad52
1 parent 3ab3ed5
commit e20ad52
Show file tree

Hide file tree

Showing 2 changed files with 1 addition and 2 deletions.
diff --git a/workflow/snakemake_rules/export_for_nextstrain.smk b/workflow/snakemake_rules/export_for_nextstrain.smk
@@ -35,7 +35,6 @@ rule all_regions:
     input:
         auspice_json = expand("auspice/{prefix}_{build_name}.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES),
         tip_frequencies_json = expand("auspice/{prefix}_{build_name}_tip-frequencies.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES),
-        root_sequence_json = expand("auspice/{prefix}_{build_name}_root-sequence.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES),
         dated_auspice_json = expand("auspice/{prefix}_{build_name}_{date}.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES, date=config.get("build_date", get_todays_date())),
         dated_tip_frequencies_json = expand("auspice/{prefix}_{build_name}_{date}_tip-frequencies.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES, date=config.get("build_date", get_todays_date())),
         dated_root_sequence_json = expand("auspice/{prefix}_{build_name}_{date}_root-sequence.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES, date=config.get("build_date", get_todays_date()))

diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk
@@ -1421,7 +1421,7 @@ rule export:
             --metadata {input.metadata} \
             --node-data {input.node_data} \
             --auspice-config {input.auspice_config} \
-            --include-root-sequence \
+            --include-root-sequence-inline \
             --colors {input.colors} \
             --lat-longs {input.lat_longs} \
             --title {params.title:q} \