correct file names for converted files where R1 and R2 are switched (inDrops v2 and v3) (32c3cd71) · Commits · github_fork / Universc

launch_universc.sh

+14 −0

Original line number	Diff line number	Diff line
		@@ -1194,6 +1194,13 @@ crR1s=()
		for fq in "${read1[@]}"; do
		to=`basename $fq`
		to="${crIN}/${to}"

		#invert read1 and read2
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]]; then
		#where converted "read1" is R2 in source files (corrected names for cellranger)
		to=`echo $to \| sed -e "s/_R2_/_R1_/g"
		fi

		crR1s+=($to)

		echo " handling $fq ..."
		@@ -1210,6 +1217,13 @@ for fq in "${read2[@]}"; do
		to=`basename $fq`
		to="${crIN}/${to}"
		to=$(echo "$to" \| sed 's/\.gz$//')

		#invert read1 and read2
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]]; then
		#where converted "read2" is R1 in source files
		to=`echo $to \| sed -e "s/_R1_/_R2_/g"
		fi

		crR2s+=($to)

		echo " handling $fq ..."