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.
nextstrain · Sep 14, 2023 · 2c192fa · 2c192fa
1 parent 10bca60
commit 2c192fa
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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} \