From 7ae5034785426e90e443053ee4faa4458f1e9d48 Mon Sep 17 00:00:00 2001
From: FriederikeHanssen <friederike.hanssen@seqera.io>
Date: Tue, 19 Nov 2024 09:06:34 +0000
Subject: [PATCH] adjust argument

---
 conf/modules/deepvariant.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules/deepvariant.config b/conf/modules/deepvariant.config
index e76317fb91..222810e21f 100644
--- a/conf/modules/deepvariant.config
+++ b/conf/modules/deepvariant.config
@@ -18,7 +18,7 @@ process {
     withName: 'DEEPVARIANT_RUNDEEPVARIANT' {
         ext.args   = [
             params.wes ?  "--model_type=WES" : "--model_type=WGS" ,
-            !params.skip_tools?.contains("baserecalibrator") ? "--call_variants_extra_args '--parse_sam_aux_fields=true,--use_original_quality_scores=true'" : ''
+            !params.skip_tools?.contains("baserecalibrator") ? "--make_examples_extra_args '--parse_sam_aux_fields=true,--use_original_quality_scores=true'" : ''
         ].join(' ').trim()
         ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.baseName}" }
         ext.when   = { params.tools && params.tools.split(',').contains('deepvariant') }