Loading launch_universc.sh +58 −5 Original line number Diff line number Diff line Loading @@ -784,7 +784,7 @@ keys=("R1" "R2") ## calling cellranger ## ## This is a work-in-progress ## ##################################### if [[ ${#index1[@]} -eq ${#read1[@]} ]] && [[ ${#index1[@]} -ge 1 ]]; then if [[ ${#index1[@]} -eq ${#read1[@]} ]] || [[ ${#index1[@]} -ge 1 ]]; then if [[ ${#index1[@]} -eq 1 ]]; then echo " index1 $index1 passes" elif [[ ${#index1[@]} -ge 2 ]]; then Loading @@ -799,7 +799,7 @@ else for ii in $(seq 1 1 ${#read1[@]}); do #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I1 filename for R1 filename #derive I1 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_I1/' ) #only add index1 files to list variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then Loading @@ -817,7 +817,7 @@ fi ##################################### # only check I2 for dual-indexed techniques if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq" ]]; then if [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then if [[ ${#index2[@]} -eq ${#read1[@]} ]] || [[ ${#index2[@]} -ge 1 ]]; then if [[ ${#index2[@]} -eq 1 ]]; then echo " index2 $index2 passes" elif [[ ${#index2[@]} -ge 2 ]]; then Loading @@ -832,7 +832,7 @@ if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ for ii in $(seq 1 1 ${#read1[@]}); do #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I2 filename for R1 filename #derive I2 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_I2/' ) #only add index2 files to list variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then Loading @@ -842,6 +842,41 @@ if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ fi fi # check for indexes in R2 and R3 (R1 -> R2; R2 -> I1; R3 -> I2; R4 -> R1) if [[ "$technology" == "indrop-v3" ]]; then if [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then echo " index I1 and I2 found for ${technology}" else #checking for R2 and R3 index files echo " checking for index R2 and R3 files..." for ii in $(seq 1 1 ${#read1[@]}); do #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I1 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R2/' ) #only add index1 files to list variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then index1+=("$indexfile") fi #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I2 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R3/' ) #only add index2 files to list variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then index2+=("$indexfile") fi #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I2 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R4/' ) #only replace R2 files with R4 variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then read2[$(( $ii -1 ))]=("$indexfile") fi done fi fi if [[ $verbose = "true" ]]; then echo "${#read1[@]} read1s: ${read1[@]}" Loading Loading @@ -1618,6 +1653,10 @@ for fq in "${read2[@]}"; do #where converted "read2" is R1 in source files echo "using transcripts in Read 1 for ${technology}" to=`echo $to | sed -e "s/_R1_/_R2_/g"` #where converted "read2" is R4 in source files if [[ "$technology" == "indrop-v3" ]]; then to=`echo $to | sed -e "s/_R4_/_R2_/g"` fi fi if [[ $verbose == true ]]; then echo "$to"; fi Loading Loading @@ -1646,6 +1685,13 @@ if [[ ${#index1[@]} -ge 1 ]]; then to="${crIN}/${to}" to=$(echo "$to" | sed 's/\.gz$//') #convert index for R2 and R3 if [[ "$technology" == "indrop-v3" ]]; then #where converted "index1" is R2 in source files (corrected names for cellranger) echo "using transcripts in Read 2 for ${technology}" to=`echo $to | sed -e "s/_R2_/_I1_/g"` fi if [[ $verbose == true ]]; then echo "$to" ; fi crI1s+=($to) Loading Loading @@ -1673,6 +1719,13 @@ if [[ ${#index2[@]} -ge 1 ]]; then to="${crIN}/${to}" to=$(echo "$to" | sed 's/\.gz$//') #convert index for R2 and R3 if [[ "$technology" == "indrop-v3" ]]; then #where converted "index2" is R3 in source files (corrected names for cellranger) echo "using transcripts in Read 2 for ${technology}" to=`echo $to | sed -e "s/_R3_/_I2_/g"` fi if [[ $verbose == true ]]; then echo "$to" ; fi crI2s+=($to) Loading Loading
launch_universc.sh +58 −5 Original line number Diff line number Diff line Loading @@ -784,7 +784,7 @@ keys=("R1" "R2") ## calling cellranger ## ## This is a work-in-progress ## ##################################### if [[ ${#index1[@]} -eq ${#read1[@]} ]] && [[ ${#index1[@]} -ge 1 ]]; then if [[ ${#index1[@]} -eq ${#read1[@]} ]] || [[ ${#index1[@]} -ge 1 ]]; then if [[ ${#index1[@]} -eq 1 ]]; then echo " index1 $index1 passes" elif [[ ${#index1[@]} -ge 2 ]]; then Loading @@ -799,7 +799,7 @@ else for ii in $(seq 1 1 ${#read1[@]}); do #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I1 filename for R1 filename #derive I1 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_I1/' ) #only add index1 files to list variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then Loading @@ -817,7 +817,7 @@ fi ##################################### # only check I2 for dual-indexed techniques if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq" ]]; then if [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then if [[ ${#index2[@]} -eq ${#read1[@]} ]] || [[ ${#index2[@]} -ge 1 ]]; then if [[ ${#index2[@]} -eq 1 ]]; then echo " index2 $index2 passes" elif [[ ${#index2[@]} -ge 2 ]]; then Loading @@ -832,7 +832,7 @@ if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ for ii in $(seq 1 1 ${#read1[@]}); do #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I2 filename for R1 filename #derive I2 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_I2/' ) #only add index2 files to list variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then Loading @@ -842,6 +842,41 @@ if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ fi fi # check for indexes in R2 and R3 (R1 -> R2; R2 -> I1; R3 -> I2; R4 -> R1) if [[ "$technology" == "indrop-v3" ]]; then if [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then echo " index I1 and I2 found for ${technology}" else #checking for R2 and R3 index files echo " checking for index R2 and R3 files..." for ii in $(seq 1 1 ${#read1[@]}); do #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I1 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R2/' ) #only add index1 files to list variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then index1+=("$indexfile") fi #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I2 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R3/' ) #only add index2 files to list variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then index2+=("$indexfile") fi #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I2 filename from R1 filename indexfile=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R4/' ) #only replace R2 files with R4 variable if file exists if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then read2[$(( $ii -1 ))]=("$indexfile") fi done fi fi if [[ $verbose = "true" ]]; then echo "${#read1[@]} read1s: ${read1[@]}" Loading Loading @@ -1618,6 +1653,10 @@ for fq in "${read2[@]}"; do #where converted "read2" is R1 in source files echo "using transcripts in Read 1 for ${technology}" to=`echo $to | sed -e "s/_R1_/_R2_/g"` #where converted "read2" is R4 in source files if [[ "$technology" == "indrop-v3" ]]; then to=`echo $to | sed -e "s/_R4_/_R2_/g"` fi fi if [[ $verbose == true ]]; then echo "$to"; fi Loading Loading @@ -1646,6 +1685,13 @@ if [[ ${#index1[@]} -ge 1 ]]; then to="${crIN}/${to}" to=$(echo "$to" | sed 's/\.gz$//') #convert index for R2 and R3 if [[ "$technology" == "indrop-v3" ]]; then #where converted "index1" is R2 in source files (corrected names for cellranger) echo "using transcripts in Read 2 for ${technology}" to=`echo $to | sed -e "s/_R2_/_I1_/g"` fi if [[ $verbose == true ]]; then echo "$to" ; fi crI1s+=($to) Loading Loading @@ -1673,6 +1719,13 @@ if [[ ${#index2[@]} -ge 1 ]]; then to="${crIN}/${to}" to=$(echo "$to" | sed 's/\.gz$//') #convert index for R2 and R3 if [[ "$technology" == "indrop-v3" ]]; then #where converted "index2" is R3 in source files (corrected names for cellranger) echo "using transcripts in Read 2 for ${technology}" to=`echo $to | sed -e "s/_R3_/_I2_/g"` fi if [[ $verbose == true ]]; then echo "$to" ; fi crI2s+=($to) Loading
