From 2017aea0637527286d2f20f6791df764366fc2ec Mon Sep 17 00:00:00 2001
From: sina <sina.majidian@gmail.com>
Date: Mon, 11 Dec 2023 13:46:24 +0100
Subject: [PATCH] lowSO/fragment-detection is  default

---
 FastOMA.nf | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/FastOMA.nf b/FastOMA.nf
index 86c28df..411c7e3 100644
--- a/FastOMA.nf
+++ b/FastOMA.nf
@@ -244,8 +244,6 @@ process hog_big{
     """
         fastoma-infer-subhogs  --input-rhog-folder ${rhogsbig}  \
                                --species-tree ${species_tree} \
-                               --fragment-detection \
-                               --low-so-detection \
                                --parallel
     """
 }
@@ -263,9 +261,7 @@ process hog_rest{
   script:
     """
         fastoma-infer-subhogs --input-rhog-folder ${rhogsrest}  \
-                              --species-tree ${species_tree} \
-                              --fragment-detection \
-                              --low-so-detection
+                              --species-tree ${species_tree}
                               #--out pickle_hogs
     """
 }