From 5e7742aed4d18af1c7162975274786e95dcb8beb Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Mon, 15 Jul 2024 13:19:10 -0400
Subject: [PATCH] Add rest of the genes for gene coverage columns (#79)

---
 ingest/defaults/config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ingest/defaults/config.yaml b/ingest/defaults/config.yaml
index d104ae4e..3afcc3af 100644
--- a/ingest/defaults/config.yaml
+++ b/ingest/defaults/config.yaml
@@ -111,7 +111,7 @@ curate:
 nextclade:
   min_length: 1000 # E gene length is approximately 1400nt
   min_seed_cover: 0.1
-  gene: ['E','NS1']
+  gene: ['E','C','M','pr','NS1','NS2A','NS2B','NS3','NS4A','2K','NS4B','NS5']
   # Nextclade Fields to rename to metadata field names.
   field_map:
     seqName: genbank_accession # ID field used to merge annotations