WIP: properly handle TSVs w/ csvtk/tsv-utils

nextstrain · Nov 26, 2024 · 0d70fe0 · 0d70fe0
1 parent f55c6c2
commit 0d70fe0
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/ingest/rules/fetch_from_ncbi.smk b/ingest/rules/fetch_from_ncbi.smk
@@ -96,12 +96,13 @@ rule format_ncbi_dataset_report:
             --package {input.dataset_package} \
             --fields {params.ncbi_datasets_fields:q} \
             --elide-header \
-            | csvtk fix-quotes -Ht \
-            | csvtk add-header -t -l -n {params.ncbi_datasets_fields:q} \
+            | csvtk add-header -t -n {params.ncbi_datasets_fields:q} \
             | csvtk rename -t -f accession -n accession_version \
             | csvtk -t mutate -f accession_version -n accession -p "^(.+?)\." \
             | csvtk del-quotes -t \
+            | csv2tsv --csv-delim $'\t' \
             | tsv-select -H -f accession --rest last \
+            | csvtk fix-quotes -t \
             > {output.ncbi_dataset_tsv}
         """