From 07813d854c67d7996409b648268fa8dde800955b Mon Sep 17 00:00:00 2001
From: Vanni Benvenga <vanni.benvenga@gmail.com>
Date: Thu, 23 Mar 2023 14:31:54 +0100
Subject: [PATCH] Update file panaroo.sh

---
 exercises/Pangenome_analysis/panaroo.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/exercises/Pangenome_analysis/panaroo.sh b/exercises/Pangenome_analysis/panaroo.sh
index b8a788f..d73272f 100644
--- a/exercises/Pangenome_analysis/panaroo.sh
+++ b/exercises/Pangenome_analysis/panaroo.sh
@@ -35,5 +35,5 @@ done
 # Runs singularity on the annotations and send the output to the output folder
 echo Starting panaroo $(date +"%T")
 cd panaroo
-$singpath/panaroo_1.3.0--pyhdfd78af_0.sif panaroo -i $wd/panaroo/annotation_files/*.gff -o ./panaroo_output/ --clean-mode strict --remove-invalid-genes
+$singpath/panaroo_1.3.0--pyhdfd78af_0.sif panaroo -i $wd/panaroo/annotation_files/*.gff -o ./panaroo_output/ --clean-mode strict --remove-invalid-genes --core_threshold
 echo Done $(date +"%T")
\ No newline at end of file
-- 
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