set check-ref to warn in bcftools norm

EBIvariation · Aug 3, 2023 · 05ca0c6 · 05ca0c6
1 parent 0580f22
commit 05ca0c6
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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
     """
 }