Loading launch_universc.sh +5 −5 Original line number Diff line number Diff line Loading @@ -683,7 +683,7 @@ elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq elif [[ "$technology" == "rambda-seq" ]] || [[ "$technology" == "lamda-seq" ]] || [[ "$technology" == "lambda-seq" ]] || [[ "$technology" == "ramdaseq" ]] || [[ "$technology" == "ram-da-seq" ]] || [[ "$technology" == "ramda-seq" ]]; then technology="ramda-seq" nonUMI=true elif [[ "$technology" == "rambda-seq-c1" ]] || [[ "$technology" == "lamda-seq-c1" ]] || [[ "$technology" == "lambda-seq-c1" ]] || [[ "$technology" == "ramdaseqc1" ]] || [[ "$technology" == "ram-da-seq-c1" ]] || [[ "$technology" == "ramda-seq-c1" ]] || [[ "$technology" == "ramda-seqc1" ]] [[ "$technology" == "c1-rambda-seq" ]] || [[ "$technology" == "c1-lamda-seq" ]] || [[ "$technology" == "c1-lambda-seq" ]] || [[ "$technology" == "c1-ramdaseq" ]] || [[ "$technology" == "c1-ram-da-seq" ]] || [[ "$technology" == "c1ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]]; then elif [[ "$technology" == "rambda-seq-c1" ]] || [[ "$technology" == "lamda-seq-c1" ]] || [[ "$technology" == "lambda-seq-c1" ]] || [[ "$technology" == "ramdaseqc1" ]] || [[ "$technology" == "ram-da-seq-c1" ]] || [[ "$technology" == "ramda-seq-c1" ]] || [[ "$technology" == "ramda-seqc1" ]] || [[ "$technology" == "c1-rambda-seq" ]] || [[ "$technology" == "c1-lamda-seq" ]] || [[ "$technology" == "c1-lambda-seq" ]] || [[ "$technology" == "c1-ramdaseq" ]] || [[ "$technology" == "c1-ram-da-seq" ]] || [[ "$technology" == "c1ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]]; then technology="c1-ramda-seq" nonUMI=true elif [[ "$technology" == "sciseq" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "sci-rna-seq" ]]; then Loading Loading @@ -1765,9 +1765,9 @@ else if [[ ! -f ${whitelistdir}/microwellseq_barcode.txt ]]; then echo " ...generating combination of I1, I2, and RT barcodes..." fi elif [[ "$technology" == "quartz-seq" ]]; elif [[ "$technology" == "quartz-seq" ]]; then indexlength=$(($(head $index1([0]) -n 2 | tail -n 1 | wc -c) -1)) if [[ -f $index2([0]) ]]; then if [[ -f $(echo ${index2}([0])) ]]; then index2length=$(($(head $index2([0]) -n 2 | tail -n 1 | wc -c) -1)) barcodelength=$(($indexlength + $index2length)) if [[ -f ${whitelistdir}/Illumina_dual_barcodes.txt ]];then Loading Loading @@ -2680,7 +2680,7 @@ else fi #C1, Quartz-Seq and RamDA-Seq: add mock UMI for non-UMI techniques elif [[ "$technology" == "fluidigm-c1" ]] || [[ "$technology" == "icell8-full-length" ]] || [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]] || [[ "$technology" == "quartz-seq" ]]; then if [[ "$technology" == "fluidigm-c1" ]] || [[ "$technology" == "icell8-full-length" ]] || [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]] || [[ "$technology" == "quartz-seq" ]]; then echo " ...processsing for ${technology}" if [[ $verbose ]]; then echo "Note: ${technology} does not contain UMIs" Loading @@ -2695,7 +2695,7 @@ else indexlength=$(($(head $index1([0]) -n 2 | tail -n 1 | wc -c) -1)) barcodelength=$indexlength #detect whether index 2 files exist if [[ -f $index2([0]) ]]; then if [[ -f $(echo ${index2}([0])) ]]; then #detect barcode length from length of both index sequences index2length=$(($(head $index2([0]) -n 2 | tail -n 1 | wc -c) -1)) barcodelength=$(($indexlength + $index2length)) Loading Loading
launch_universc.sh +5 −5 Original line number Diff line number Diff line Loading @@ -683,7 +683,7 @@ elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq elif [[ "$technology" == "rambda-seq" ]] || [[ "$technology" == "lamda-seq" ]] || [[ "$technology" == "lambda-seq" ]] || [[ "$technology" == "ramdaseq" ]] || [[ "$technology" == "ram-da-seq" ]] || [[ "$technology" == "ramda-seq" ]]; then technology="ramda-seq" nonUMI=true elif [[ "$technology" == "rambda-seq-c1" ]] || [[ "$technology" == "lamda-seq-c1" ]] || [[ "$technology" == "lambda-seq-c1" ]] || [[ "$technology" == "ramdaseqc1" ]] || [[ "$technology" == "ram-da-seq-c1" ]] || [[ "$technology" == "ramda-seq-c1" ]] || [[ "$technology" == "ramda-seqc1" ]] [[ "$technology" == "c1-rambda-seq" ]] || [[ "$technology" == "c1-lamda-seq" ]] || [[ "$technology" == "c1-lambda-seq" ]] || [[ "$technology" == "c1-ramdaseq" ]] || [[ "$technology" == "c1-ram-da-seq" ]] || [[ "$technology" == "c1ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]]; then elif [[ "$technology" == "rambda-seq-c1" ]] || [[ "$technology" == "lamda-seq-c1" ]] || [[ "$technology" == "lambda-seq-c1" ]] || [[ "$technology" == "ramdaseqc1" ]] || [[ "$technology" == "ram-da-seq-c1" ]] || [[ "$technology" == "ramda-seq-c1" ]] || [[ "$technology" == "ramda-seqc1" ]] || [[ "$technology" == "c1-rambda-seq" ]] || [[ "$technology" == "c1-lamda-seq" ]] || [[ "$technology" == "c1-lambda-seq" ]] || [[ "$technology" == "c1-ramdaseq" ]] || [[ "$technology" == "c1-ram-da-seq" ]] || [[ "$technology" == "c1ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]]; then technology="c1-ramda-seq" nonUMI=true elif [[ "$technology" == "sciseq" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "sci-rna-seq" ]]; then Loading Loading @@ -1765,9 +1765,9 @@ else if [[ ! -f ${whitelistdir}/microwellseq_barcode.txt ]]; then echo " ...generating combination of I1, I2, and RT barcodes..." fi elif [[ "$technology" == "quartz-seq" ]]; elif [[ "$technology" == "quartz-seq" ]]; then indexlength=$(($(head $index1([0]) -n 2 | tail -n 1 | wc -c) -1)) if [[ -f $index2([0]) ]]; then if [[ -f $(echo ${index2}([0])) ]]; then index2length=$(($(head $index2([0]) -n 2 | tail -n 1 | wc -c) -1)) barcodelength=$(($indexlength + $index2length)) if [[ -f ${whitelistdir}/Illumina_dual_barcodes.txt ]];then Loading Loading @@ -2680,7 +2680,7 @@ else fi #C1, Quartz-Seq and RamDA-Seq: add mock UMI for non-UMI techniques elif [[ "$technology" == "fluidigm-c1" ]] || [[ "$technology" == "icell8-full-length" ]] || [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]] || [[ "$technology" == "quartz-seq" ]]; then if [[ "$technology" == "fluidigm-c1" ]] || [[ "$technology" == "icell8-full-length" ]] || [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]] || [[ "$technology" == "quartz-seq" ]]; then echo " ...processsing for ${technology}" if [[ $verbose ]]; then echo "Note: ${technology} does not contain UMIs" Loading @@ -2695,7 +2695,7 @@ else indexlength=$(($(head $index1([0]) -n 2 | tail -n 1 | wc -c) -1)) barcodelength=$indexlength #detect whether index 2 files exist if [[ -f $index2([0]) ]]; then if [[ -f $(echo ${index2}([0])) ]]; then #detect barcode length from length of both index sequences index2length=$(($(head $index2([0]) -n 2 | tail -n 1 | wc -c) -1)) barcodelength=$(($indexlength + $index2length)) Loading
