Ingest: Use augur merge (#60)

Use augur merge to comply with pathogen repo guide nextstrain/pathogen-repo-guide@3fc3e65

Co-authored-by: DOH-LMT2303 <[email protected]>

ingest/defaults/config.yaml

@@ -134,6 +134,7 @@ curate:
 nextclade:
   nextclade_dataset_path: '../nextclade/dataset'
   nextclade_field: 'clade_membership'
+  nextclade_id: 'accession'
 
 pathoplexus:
   URL: 'https://lapis.pathoplexus.org/west-nile/sample/details'

ingest/rules/nextclade.smk

@@ -97,24 +97,28 @@ rule select_nextclade_columns:
         """
 
 rule append_nextclade_columns:
-    #Append the nextclade results to the metadata
+    """
+    Append the nextclade results to the metadata
+    """
     input:
         metadata="data/raw_metadata.tsv",
         nextclade_subtypes="data/nextclade_clades.tsv",
     output:
         metadata_all="data/metadata_nextclade.tsv",
     params:
         id_field=config["curate"]["output_id_field"],
-        nextclade_field=config["nextclade"]["nextclade_field"],
+        nextclade_id_field=config["nextclade"]["nextclade_id"],
     shell:
-        """
-        tsv-join -H \
-            --filter-file {input.nextclade_subtypes} \
-            --key-fields {params.id_field} \
-            --append-fields {params.nextclade_field} \
-            --write-all ? \
-            {input.metadata} \
-        > {output.metadata_all}
+        r"""
+        augur merge \
+            --metadata \
+                metadata={input.metadata:q} \
+                nextclade={input.nextclade_subtypes:q} \
+            --metadata-id-columns \
+                metadata={params.id_field:q} \
+                nextclade={params.nextclade_id_field:q} \
+            --output-metadata {output.metadata_all:q} \
+            --no-source-columns
         """
 
 rule append_pathoplexus_columns: