From 05ca0c6ba44db83a87580d2073f1dcf5cc6dd7c0 Mon Sep 17 00:00:00 2001
From: April Shen <ashen@ebi.ac.uk>
Date: Thu, 3 Aug 2023 12:38:49 +0100
Subject: [PATCH] set check-ref to warn in bcftools norm

---
 eva_submission/nextflow/prepare_brokering.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eva_submission/nextflow/prepare_brokering.nf b/eva_submission/nextflow/prepare_brokering.nf
index 7b7fe5d..aeaac2d 100644
--- a/eva_submission/nextflow/prepare_brokering.nf
+++ b/eva_submission/nextflow/prepare_brokering.nf
@@ -140,7 +140,7 @@ process normalise_vcf {
     trap 'if [[ \$? == 1 || \$? == 139 || \$? == 255 ]]; then exit 0; fi' EXIT
 
     mkdir normalised_vcfs
-    $params.executable.bcftools norm --no-version -f $fasta -O z -o normalised_vcfs/$vcf_file $vcf_file 2> normalised_vcfs/${vcf_file.getBaseName()}_bcftools_norm.log
+    $params.executable.bcftools norm --no-version -cw -f $fasta -O z -o normalised_vcfs/$vcf_file $vcf_file 2> normalised_vcfs/${vcf_file.getBaseName()}_bcftools_norm.log
     $params.executable.bcftools index -c normalised_vcfs/$vcf_file
     """
 }