diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf
index 817abcb523d..8ff8d90a11f 100644
--- a/modules/nf-core/manta/somatic/main.nf
+++ b/modules/nf-core/manta/somatic/main.nf
@@ -37,8 +37,9 @@ process MANTA_SOMATIC {
         --tumorBam $input_tumor \
         --normalBam $input_normal \
         --reference $fasta \
+        --runDir manta \
         $options_manta \
-        --runDir manta
+        $args
 
     python manta/runWorkflow.py -m local -j $task.cpus
 
diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf
index 3d8b8b9c840..e3d6ca1b142 100644
--- a/modules/nf-core/manta/tumoronly/main.nf
+++ b/modules/nf-core/manta/tumoronly/main.nf
@@ -33,8 +33,9 @@ process MANTA_TUMORONLY {
     configManta.py \
         --tumorBam $input \
         --reference $fasta \
+        --runDir manta \
         $options_manta \
-        --runDir manta
+        $args
 
     python manta/runWorkflow.py -m local -j $task.cpus