From eb3b0a59a7becb0293f67ca164b5607ffe434045 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Wed, 18 Dec 2024 13:51:12 -0800
Subject: [PATCH] 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
---
 ingest/rules/curate.smk          | 5 +++--
 ingest/rules/fetch_from_ncbi.smk | 8 +++-----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/ingest/rules/curate.smk b/ingest/rules/curate.smk
index d871be2..8c3ae25 100644
--- 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
index 9718dcf..b8f595d 100644
--- 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}
         """