correct renaming files (f65ce8bb) · Commits · github_fork / Universc

launch_universc.sh

+5 −5

Original line number	Diff line number	Diff line
		@@ -488,15 +488,15 @@ for i in {1..2}; do
		echo "*Warning: file $read does not have lane value in its name. Lane 1 is assumed.*"
		echo " renaming $read ..."
		fi
		rename "s/_$raadkey/_L001_$readkey/" $read
		rename "s/_$readkey/_L001_$readkey/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_${readkey}/_L001_${raedkey}/g"`
		read=`echo $read \| sed -e "s/_${readkey}/_L001_${readkey}/g"`
		list[$j]=$read
		;;
		esac
		case $read in
		#check if contains sample before lane
		_S[123456789]_L0)
		_S[0123456789]_L0)
		if [[ $verbose == "true" ]]; then
		echo " $read compatible with sample"
		fi
		@@ -510,7 +510,7 @@ for i in {1..2}; do
		k=$((${j}+1))
		rename "s/_L0/_S${k}_L0/" $read
		#update file variable
		read=`echo $read \| sed -e "s/_L0/_S${j}_L0/g"`
		read=`echo $read \| sed -e "s/_L0/_S${k}_L0/g"`
		list[$j]=$read
		;;
		esac
		@@ -529,7 +529,7 @@ for i in {1..2}; do
		fi
		rename "s/_${readkey}.*\./_${readkey}_001\./" $read
		#update file variable
		read=`echo $read \| sed -e "s/_${readkey}.*\./_${raedkey}_001\./g"`
		read=`echo $read \| sed -e "s/_${readkey}.*\./_${readkey}_001\./g"`
		list[$j]=$read
		;;
		esac