diff --git a/app/src/main/java/com/mobilegenomics/f5n/core/Argument.java b/app/src/main/java/com/mobilegenomics/f5n/core/Argument.java
index fdace6c5..78e2c45c 100644
--- a/app/src/main/java/com/mobilegenomics/f5n/core/Argument.java
+++ b/app/src/main/java/com/mobilegenomics/f5n/core/Argument.java
@@ -124,7 +124,7 @@ public String toString() {
                     return this.argValue;
                 }
             } else {
-                return this.flag;
+                return this.flagOnly ? this.flag : "";
             }
         }
         return "";
diff --git a/app/src/main/res/raw/minimap2.json b/app/src/main/res/raw/minimap2.json
index 9a523e39..b5812bf4 100644
--- a/app/src/main/res/raw/minimap2.json
+++ b/app/src/main/res/raw/minimap2.json
@@ -2,7 +2,7 @@
   "args": [
     {
       "argName": "Temporary Prefix for multi-part index",
-      "argValue": "temp.minimap",
+      "argValue": null,
       "argDescription": "Prefix to create temporary files. Typically used for a multi-part index",
       "flag": "--multi-prefix=",
       "argID": "MINIMAP2_TEMP_FILE",