diff --git a/ingest/Snakefile b/ingest/Snakefile
index c0ffca99..46f4585d 100644
--- a/ingest/Snakefile
+++ b/ingest/Snakefile
@@ -64,7 +64,6 @@ 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"):
diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
deleted file mode 100644
index 57b250b7..00000000
--- a/ingest/workflow/snakemake_rules/nextclade.smk
+++ /dev/null
@@ -1,68 +0,0 @@
-
-rule nextclade_dataset:
-    output:
-        temp("mpxv.zip"),
-    shell:
-        """
-        nextclade dataset get --name MPXV --output-zip {output}
-        """
-
-
-rule nextclade_dataset_hMPXV:
-    output:
-        temp("hmpxv.zip"),
-    shell:
-        """
-        nextclade dataset get --name hMPXV --output-zip {output}
-        """
-
-
-rule align:
-    input:
-        sequences="data/sequences.fasta",
-        dataset="hmpxv.zip",
-    output:
-        alignment="data/alignment.fasta",
-        insertions="data/insertions.csv",
-        translations="data/translations.zip",
-    params:
-        translations=lambda w: "data/translations/{gene}.fasta",
-    threads: 4
-    shell:
-        """
-        nextclade run -D {input.dataset} -j {threads}   --retry-reverse-complement \
-                  --output-fasta {output.alignment}  --output-translations {params.translations} \
-                  --output-insertions {output.insertions} {input.sequences}
-        zip -rj {output.translations} data/translations
-        """
-
-
-rule nextclade:
-    input:
-        sequences="data/sequences.fasta",
-        dataset="mpxv.zip",
-    output:
-        "data/nextclade.tsv",
-    threads: 4
-    shell:
-        """
-        nextclade run -D {input.dataset} -j {threads} --output-tsv {output}  {input.sequences}  --retry-reverse-complement
-        """
-
-
-rule join_metadata_clades:
-    input:
-        nextclade="data/nextclade.tsv",
-        metadata="data/metadata_raw.tsv",
-    output:
-        "data/metadata.tsv",
-    params:
-        id_field=config["transform"]["id_field"],
-    shell:
-        """
-        python3 bin/join-metadata-and-clades.py \
-                --id-field {params.id_field} \
-                --metadata {input.metadata} \
-                --nextclade {input.nextclade} \
-                -o {output}
-        """
diff --git a/ingest/workflow/snakemake_rules/transform.smk b/ingest/workflow/snakemake_rules/transform.smk
index 079a90e0..1adc9bc1 100644
--- a/ingest/workflow/snakemake_rules/transform.smk
+++ b/ingest/workflow/snakemake_rules/transform.smk
@@ -41,7 +41,7 @@ rule transform:
         sequences_ndjson="data/sequences.ndjson",
         all_geolocation_rules="data/all-geolocation-rules.tsv",
     output:
-        metadata="data/metadata_raw.tsv",
+        metadata="data/metadata.tsv",
         sequences="data/sequences.fasta",
     log:
         "logs/transform.txt",