From 2c192fa6184da971c91d4a7b69a931fbe0978cfa Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Thu, 14 Sep 2023 11:49:56 -0700
Subject: [PATCH] Make the choice of "accession" on the config level

Don't set defaults when retrieving strain_id_field so "accession" is
only set on the config level.
---
 workflow/snakemake_rules/core.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/snakemake_rules/core.smk b/workflow/snakemake_rules/core.smk
index 402203c..3f85fdd 100644
--- a/workflow/snakemake_rules/core.smk
+++ b/workflow/snakemake_rules/core.smk
@@ -10,7 +10,7 @@ rule wrangle_metadata:
     output:
         metadata="data/{a_or_b}/metadata_by_accession.tsv",
     params:
-        strain_id=config.get("strain_id_field", "strain"),
+        strain_id=config["strain_id_field"],
     shell:
         """
         python3 scripts/wrangle_metadata.py --metadata {input.metadata} \