fixup replace: more efficient joining

This change bypasses the APPEND_FIELDS and the intermediate nextclade_renamed.tsv file.

Co-authored-by: Jover Lee <[email protected]>

ingest/workflow/snakemake_rules/nextclade.smk

@@ -73,16 +73,13 @@ rule join_metadata_clades:
             -p '(.+)' \
             -r '{{kv}}' \
             -k {input.nextclade_field_map} \
-            > data/nextclade_renamed.tsv
-
-        export APPEND_FIELDS=`awk 'NR>1 {{print $2}}' {input.nextclade_field_map} | grep -v "seqName" | tr '\n' ',' | sed 's/,$//g'`
-
-        tsv-join -H \
-            --filter-file data/nextclade_renamed.tsv \
+        | tsv-join -H \
+            --filter-file - \
             --key-fields seqName \
             --data-fields {params.id_field} \
-            --append-fields $APPEND_FIELDS \
+            --append-fields '*' \
             --write-all ? \
             {input.metadata} \
+        | tsv-select -H --exclude seqName \
             > {output.metadata}
         """