From a6df20f0e8540a60a403eab81d80e517d1e31ee0 Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Mon, 14 Aug 2023 15:58:26 -0700
Subject: [PATCH] fixup! Use "accession" column as ID column directly

---
 Snakefile | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/Snakefile b/Snakefile
index 245107e6..0549509e 100644
--- a/Snakefile
+++ b/Snakefile
@@ -83,18 +83,6 @@ rule decompress:
         zstd -d -c {input.metadata} > {output.metadata}
         """
 
-# rule wrangle_metadata:
-#     input:
-#         metadata="data/metadata_{serotype}.tsv",
-#     output:
-#         metadata="results/wrangled_metadata_{serotype}.tsv",
-#     params:
-#         strain_id=config.get("strain_id_field", "strain"), #accession
-#     shell:
-#         """
-#         csvtk -t rename -f strain -n strain_original {input.metadata} \
-#           | csvtk -t mutate -f {params.strain_id} -n strain > {output.metadata}
-#         """
 
 rule filter:
     """