From 44fa492c1fdf3a614cabb3eb3ace67d3ab8e2e95 Mon Sep 17 00:00:00 2001
From: czerno <fotakisg@gmail.com>
Date: Thu, 20 May 2021 21:02:10 +0200
Subject: [PATCH] -v -S flags for singularity

---
 NeoFuse | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/NeoFuse b/NeoFuse
index 1a9bb97..f08a0fd 100755
--- a/NeoFuse
+++ b/NeoFuse
@@ -388,12 +388,12 @@ if [ "$BUILD" == "false" ]; then
 					exit 1
 				fi
 				if [ "$IN" != "" ]; then
-					singularity exec --no-home $SMOUNT $DIR"/NeoFuse.sif" NeoFuse_multi -i $IN -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT -C $CUSTOMLIST -k $KEEPBAM -K $FUSIONFILE -f $ARRIBAFILTERS
+					singularity exec --no-home $SMOUNT $DIR"/NeoFuse.sif" NeoFuse_multi -i $IN -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT -C $CUSTOMLIST -k $KEEPBAM -K $FUSIONFILE -f $ARRIBAFILTERS -v $VARIANTSFILE -S $GENEBREAK
 				elif [ "$READ1" != "" ]; then
 					if [ "$READ2" == "" ]; then
-						singularity exec --no-home $SMOUNT $DIR"/NeoFuse.sif" NeoFuse_single -1 $READ1 -d $ID -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT -C $CUSTOMLIST -k $KEEPBAM -K $FUSIONFILE -f $ARRIBAFILTERS
+						singularity exec --no-home $SMOUNT $DIR"/NeoFuse.sif" NeoFuse_single -1 $READ1 -d $ID -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT -C $CUSTOMLIST -k $KEEPBAM -K $FUSIONFILE -f $ARRIBAFILTERS -v $VARIANTSFILE -S $GENEBREAK
 					else
-						singularity exec --no-home $SMOUNT $DIR"/NeoFuse.sif" NeoFuse_single -1 $READ1 -2 $READ2 -d $ID -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -T $RANK -t $THRESHOLD -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT -C $CUSTOMLIST -k $KEEPBAM -K $FUSIONFILE -f $ARRIBAFILTERS
+						singularity exec --no-home $SMOUNT $DIR"/NeoFuse.sif" NeoFuse_single -1 $READ1 -2 $READ2 -d $ID -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -T $RANK -t $THRESHOLD -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT -C $CUSTOMLIST -k $KEEPBAM -K $FUSIONFILE -f $ARRIBAFILTERS -v $VARIANTSFILE -S $GENEBREAK
 					fi
 				else
 					echo "Invalid arguments"