-v -S flags for singularity

icbi-lab · May 20, 2021 · 44fa492 · 44fa492
1 parent 93321b4
commit 44fa492
Showing 1 changed file with 3 additions and 3 deletions.
diff --git 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"