made the input file for each run unique. (b88fdcf8) · Commits · github_fork / Universc

launch_universc.sh

+23 −29

Original line number	Diff line number	Diff line
		@@ -530,6 +530,10 @@ if [[ -z $id ]]; then
		exit 1
		fi
		fi
		crIN=${crIN}_$id
		if [[ ! -d ${crIN} ]]; then
		convert=true
		fi
		##########


		@@ -785,11 +789,8 @@ fi
		echo "creating a folder for all cellranger input files ..."
		convFiles=()

		if [[ ! -d $crIN ]] \|\| [[ $lastcall != $technology ]]; then
		if [[ ! -d $crIN ]]; then
		echo " directory $crIN created for converted files"
		if [[ -d $crIN ]]; then
		rm -rf $crIN
		fi
		mkdir $crIN
		else
		echo " directory $crIN already exists"
		@@ -803,17 +804,14 @@ crR1s=()
		for fq in "${read1[@]}"; do
		to=`basename $fq`
		to="${crIN}/${to}"
		to=$(echo "$to" \| sed 's/\.gz$//')
		crR1s+=($to)

		if [[ $convert == "true" ]]; then
		echo " handling $fq ..."
		convFiles+=($to)
		if [[ $fq == *'.gz' ]]; then
		gunzip -c $fq > $to
		else
		cp -T $fq $to
		if [[ ! -f $to ]] \|\| [[ $convert == "true" ]]; then
		cp -f $fq $to
		fi
		if [[ $convert == "true" ]]; then
		convFiles+=($to)
		fi
		done

		@@ -824,13 +822,9 @@ for fq in "${read2[@]}"; do
		to=$(echo "$to" \| sed 's/\.gz$//')
		crR2s+=($to)

		if [[ $convert == "true" ]]; then
		echo " handling $fq ..."
		if [[ $fq == *'.gz' ]]; then
		gunzip -c $fq > $to
		else
		cp -T $fq $to
		fi
		if [[ ! -f $to ]] \|\| [[ $convert == "true" ]]; then
		cp -f $fq $to
		fi
		done
		##########