diff --git a/workflow/main.nf b/workflow/main.nf
index 5158e81a84006c1c6aa30ad1f0e7ee149c62eec8..a55b880919efc85a558d5f71ba267bf35cdc279a 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -104,7 +104,7 @@ process starfusion {
   params.fusion == 'detect' && params.pairs == 'pe'
   script:
   """
-  bash $baseDir/process_scripts/alignment/starfusion.sh -p ${pair_id} -r ${index_path} -a ${fq1} -b ${fq2}
+  bash $baseDir/process_scripts/alignment/starfusion.sh -p ${pair_id} -r ${index_path} -a ${fq1} -b ${fq2} -m trinity -f
   """
 }