diff --git a/conf/modules.config b/conf/modules.config
index 687fd4e..70e85c8 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -229,6 +229,7 @@ process {
             enabled: false
         ]
         ext.prefix = { "${meta.id}_merged" }
+        ext.args = "--tmpdir ./"
     }
 
     withName: 'PAIRTOOLS_SPLIT' {