update renaming compatilibility with file suffices (169d27bb) · Commits · github_fork / Universc

launch_universc.sh

+3 −3

Original line number	Diff line number	Diff line
		@@ -1040,7 +1040,7 @@ for key in ${keys[@]}; do
		echo "*Warning: file $read does not have lane value in its name. Lane 1 is assumed.*"
		echo " renaming $read ..."
		fi
		rename -f "s/_$readkey/_L001_$readkey/" $read
		rename -f "s/_$readkey/_L001_$readkey/" ${read}*
		#update file variable
		read=`echo $read \| sed -e "s/_${readkey}/_L001_${readkey}/g"`
		list[$j]=$read
		@@ -1060,7 +1060,7 @@ for key in ${keys[@]}; do
		echo " renaming $read ..."
		fi
		k=$((${j}+1))
		rename -f "s/_L0/_S${k}_L0/" $read
		rename -f "s/_L0/_S${k}_L0/" ${read}*
		#update file variable
		read=`echo $read \| sed -e "s/_L0/_S${k}_L0/g"`
		list[$j]=$read
		@@ -1079,7 +1079,7 @@ for key in ${keys[@]}; do
		echo "*Warning: file $read does not have suffix in its name. Suffix 001 is given.*"
		echo " renaming $read ..."
		fi
		rename -f "s/_${readkey}.*\./_${readkey}_001\./" $read
		rename -f "s/_${readkey}.\./_${readkey}_001\./" ${read}
		#update file variable
		read=`echo $read \| sed -e "s/_${readkey}.*\./_${readkey}_001\./g"`
		list[$j]=$read

+2 −0

Original line number	Diff line number	Diff line
		@@ -18,6 +18,8 @@ if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
		fi

		unpigz -k test/shared/dropseq-test/SRR1873277*fastq.gz

		## test drop-seq data
		# unzip input data
		if [[ -f test/shared/dropseq-test/*fastq.gz ]]; then