reformat script (4dd4d9d6) · Commits · github_fork / Universc

launch_universc.sh

+16 −8

Original line number	Diff line number	Diff line
		@@ -1193,6 +1193,9 @@ if [[ $convert == "true" ]]; then
		fi

		crR1s=()
		if [[ $verbose == true]]; then
		echo "${read1[@]}"
		fi
		for fq in "${read1[@]}"; do
		to=`basename $fq`
		to="${crIN}/${to}"
		@@ -1200,6 +1203,7 @@ for fq in "${read1[@]}"; do
		#invert read1 and read2
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]]; then
		#where converted "read1" is R2 in source files (corrected names for cellranger)
		echo "using transcripts in Read 2 for ${technology}"
		to=`echo $to \| sed -e "s/_R2_/_R1_/g"
		fi

		@@ -1215,6 +1219,9 @@ for fq in "${read1[@]}"; do
		done

		crR2s=()
		if [[ $verbose == true]]; then
		echo "${read2[@]}"
		fi
		for fq in "${read2[@]}"; do
		to=`basename $fq`
		to="${crIN}/${to}"
		@@ -1223,6 +1230,7 @@ for fq in "${read2[@]}"; do
		#invert read1 and read2
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]]; then
		#where converted "read2" is R1 in source files
		echo "using transcripts in Read 1 for ${technology}"
		to=`echo $to \| sed -e "s/_R1_/_R2_/g"
		fi