changed crIN (d70680dc) · Commits · github_fork / Universc

launch_universc.sh

+11 −1

Original line number	Diff line number	Diff line
		@@ -90,7 +90,7 @@ lockfile=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock #path for .lo
		lastcallfile=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called #path for .last_called
		lastcall=`cat $lastcallfile`
		barcodefolder=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes #folder with the barcodes
		cdrIN="input4cellranger" #name of the directory with all FASTQ files given to cellranger
		crIN=input4cellranger #name of the directory with all FASTQ files given to cellranger

		#variable options
		setup=false
		@@ -301,6 +301,16 @@ fi

		#check for file type (extension) for files
		##allows incomplete file names and processing compressed files

		#test
		#read12=( $read1, $read2 )
		#for i in ${read12[@]}; do
		# echo "KAI! $i"
		#done




		for i in ${!read1[@]}; do
		read=${read1[$i]}
		if [[ $verbose == "true" ]]; then