ingest: Merge Nextclade metadata with augur merge

Modified from <nextstrain/measles@4d73b7f>
nextstrain · Oct 19, 2024 · 54ca356 · 54ca356
1 parent 1234479
commit 54ca356
Showing 1 changed file with 26 additions and 14 deletions.
diff --git a/ingest/rules/nextclade.smk b/ingest/rules/nextclade.smk
@@ -54,14 +54,12 @@ if isinstance(config["nextclade"]["field_map"], str):
         )
 
 
-rule join_metadata_clades:
+rule nextclade_metadata:
     input:
         nextclade="results/nextclade.tsv",
-        metadata="data/subset_metadata.tsv",
     output:
-        metadata="results/metadata.tsv",
+        nextclade_metadata=temp("results/nextclade_metadata.tsv"),
     params:
-        id_field=config["curate"]["id_field"],
         nextclade_id_field=config["nextclade"]["id_field"],
         nextclade_field_map=[
             f"{old}={new}" for old, new in config["nextclade"]["field_map"].items()
@@ -74,14 +72,28 @@ rule join_metadata_clades:
             --metadata - \
             --id-column {params.nextclade_id_field:q} \
             --field-map {params.nextclade_field_map:q} \
-            --output-metadata - \
-        | tsv-join -H \
-            --filter-file - \
-            --key-fields {params.nextclade_id_field} \
-            --data-fields {params.id_field} \
-            --append-fields '*' \
-            --write-all ? \
-            {input.metadata} \
-        | tsv-select -H --exclude {params.nextclade_id_field} \
-            > {output.metadata}
+            --output-metadata {output.nextclade_metadata:q}
+        """
+
+
+rule join_metadata_and_nextclade:
+    input:
+        metadata="data/subset_metadata.tsv",
+        nextclade_metadata="results/nextclade_metadata.tsv",
+    output:
+        metadata="results/metadata.tsv",
+    params:
+        metadata_id_field=config["curate"]["id_field"],
+        nextclade_id_field=config["nextclade"]["id_field"],
+    shell:
+        r"""
+        augur merge \
+            --metadata \
+                metadata={input.metadata:q} \
+                nextclade={input.nextclade_metadata:q} \
+            --metadata-id-columns \
+                metadata={params.metadata_id_field:q} \
+                nextclade={params.nextclade_id_field:q} \
+            --output-metadata {output.metadata:q} \
+            --no-source-columns
         """