ingest/nextclade: Wrap csvtk with fix-quotes/del-quotes

Similar to c0b9e50 we want to make sure csvtk does the right with the TSV file.
nextstrain · Jul 13, 2024 · dc9ac25 · dc9ac25
1 parent b6f07a6
commit dc9ac25
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/ingest/rules/nextclade.smk b/ingest/rules/nextclade.smk
@@ -75,14 +75,16 @@ rule join_metadata_and_nextclade:
         """
         export SUBSET_FIELDS=`grep -v '^#' {input.nextclade_field_map} | awk '{{print $1}}' | tr '\n' ',' | sed 's/,$//g'`
 
-        csvtk -tl cut -f $SUBSET_FIELDS \
+        csvtk fix-quotes -Ht \
             {input.nextclade} \
-        | csvtk -tl rename2 \
+        | csvtk -t cut -f $SUBSET_FIELDS \
+        | csvtk -t rename2 \
             -F \
             -f '*' \
             -p '(.+)' \
             -r '{{kv}}' \
             -k {input.nextclade_field_map} \
+        | csvtk del-quotes -t \
         | tsv-join -H \
             --filter-file - \
             --key-fields {params.nextclade_id_field} \