fix keep (4e76659a) · Commits · github_fork / Universc

launch_universc.sh

+4 −4

Original line number	Diff line number	Diff line
		@@ -752,7 +752,7 @@ if [ -d $crIN ]
		then
		echo "warning: converted $read file already exists"
		fi
		if [ ! keep ]
		if [ ! $keep ]
		then
		echo "file $crIN/$read removed"
		rm -rf $crIN/$read
		@@ -767,7 +767,7 @@ if [ -d $crIN ]
		then
		echo "warning: converted $read file already exists"
		fi
		if [ ! keep ]
		if [ ! $keep ]
		then
		echo "file $crIN/$read removed"
		rm -rf $crIN/$read
		@@ -787,7 +787,7 @@ for fq in "${read1[@]}"; do
		if [[ $fq == *'.gz' ]]; then
		echo " unzipping and redirecting $fq file..."
		gunzip -c $fq > $to
		elif [ ! keep ]
		elif [ ! $keep ]
		then
		echo " redirecting $fq file..."
		cp $fq $to
		@@ -814,7 +814,7 @@ for fq in "${read2[@]}"; do
		if [[ $fq == *'.gz' ]]; then
		echo " unzipping and redirecting $fq file..."
		gunzip -c $fq > $to
		elif [ ! keep ]
		elif [ ! $keep ]
		then
		echo " redirecting $fq file..."
		cp $fq $to