use extra flag

Author: FriederikeHanssen

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") ? "--parse_sam_aux_fields --use_original_quality_scores" : ''
+            !params.skip_tools?.contains("baserecalibrator") ? "--call_variants_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') }