Remove Nextclade related rules

Temporary removal of Nextclade-related rules, pending the compilation of a Nextclade dengue dataset and potential v3 changes. May be added back in later.
nextstrain · Oct 12, 2023 · b1b4074 · b1b4074
1 parent 74d1c11
commit b1b4074
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Showing 4 changed files with 1 addition and 149 deletions.
diff --git a/ingest/Snakefile b/ingest/Snakefile
@@ -70,7 +70,6 @@ rule all:
 
 include: "workflow/snakemake_rules/fetch_sequences.smk"
 include: "workflow/snakemake_rules/transform.smk"
-include: "workflow/snakemake_rules/nextclade.smk"
 
 
 if config.get("upload", False):

diff --git a/ingest/bin/join-metadata-and-clades.py b/ingest/bin/join-metadata-and-clades.py
diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
diff --git a/ingest/workflow/snakemake_rules/transform.smk b/ingest/workflow/snakemake_rules/transform.smk
@@ -42,7 +42,7 @@ rule transform:
         all_geolocation_rules="data/all-geolocation-rules.tsv",
         annotations=config["transform"]["annotations"],
     output:
-        metadata="data/metadata_raw.tsv",
+        metadata="data/metadata.tsv",
         sequences="data/sequences.fasta",
     log:
         "logs/transform.txt",