From 88e1f22fc966a95e003ee8e7391d5dc0d9c1cbb4 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 2 May 2019 21:00:09 -0500
Subject: [PATCH] adding new trinity

---
 workflow/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/main.nf b/workflow/main.nf
index 5158e81..a55b880 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
   """
 }
 
-- 
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