Standardize csvtk and tk-utils usage [#23]

* Wrap tsv-utils usage in `csv2tk --csv-delim $'\t'` / `csvtk fix-quotes --tabs` * Remove `csvtk fix-quotes` at start of pipeline in "format_ncbi_dataset_report" rule * Remove '-l' flag in "format_ncbi_dataset_report" rule
nextstrain · Dec 19, 2024 · eb3b0a5 · eb3b0a5
1 parent a08660b
commit eb3b0a5
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/ingest/rules/curate.smk b/ingest/rules/curate.smk
@@ -125,6 +125,7 @@ rule subset_curated_metadata_columns:
         metadata_fields=",".join(config["curate"]["metadata_columns"]),
     shell:
         r"""
-        tsv-select -H -f {params.metadata_fields} \
-            {input.metadata} > {output.metadata}
+        csvtk cut -t -f {params.metadata_fields} \
+          {input.metadata} \
+        > {output.metadata}
         """
diff --git a/ingest/rules/fetch_from_ncbi.smk b/ingest/rules/fetch_from_ncbi.smk
@@ -89,12 +89,10 @@ rule format_ncbi_dataset_report:
             --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 \
-            | tsv-select -H -f accession --rest last \
-            > {output.ncbi_dataset_tsv}
+            | csvtk -t mutate -f accession_version -n accession -p "^(.+?)\." --at 1 \
+          > {output.ncbi_dataset_tsv}
         """