Loading launch_universc.sh +48 −8 Original line number Diff line number Diff line Loading @@ -870,9 +870,9 @@ if [[ $setup == "false" ]]; then for j in ${!r1_list[@]}; do read=${r1_list[$j]} R1_file=$read R2_file=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R2/' ) R4_file=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R4/' ) I1_file=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_I1/' ) R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' ) R4_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R4/' ) I1_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' ) if [[ -f $R4_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fq') ]]; then if [[ $verbose ]]; then echo " file $R4_file found, replacing $R1_file ..." Loading Loading @@ -919,9 +919,49 @@ if [[ $setup == "false" ]]; then #only check I2 for dual-indexed techniques if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq" ]]; then if [[ ${#index2[@]} -ne ${#read1[@]} ]]; then if [[ ${#index2[@]} -gt 0 ]]; then echo " Error: number of index1 files is not matching the number of index2 files" echo " for $technology, either give no index files or give index1 and index2 for each and every read1 and read2 file" exit 1 else if [[ $verbose ]] then echo " No index files given. Automatically detecing from R1 and R2 file names..." fi r1_list=("${read1[@]}") r2_list=("${read2[@]}") i2_list=() for j in ${!r1_list[@]}; do read=${r1_list[$j]} R1_file=$read R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' ) R3_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R3/' ) I2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' ) if [[ -f $R3_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fq') ]]; then if [[ $verbose ]]; then echo " file $R3_file found, replacing $I2_file ..." fi i2_read=$R3_file i2_list[$j]=$i1_read fi if [[ -f $I2_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fq') ]]; then if [[ $verbose ]]; then echo " file $I2_file found..." fi i2_read=$I2_file i2_list[$j]=$i2_read fi done if [ ${#i2_list[@]} -eq 0 ]; then if [[ $verbose ]]; then echo "Dual index files not found" fi else if [ ${#i2_list[@]} -eq 0 ]; then if [[ $verbose ]]; then echo "echo " index files found ${#index2[@]} I2s: ${index2[@]}" fi fi fi fi elif [[ ${#index2[@]} -gt 0 ]]; then echo " Error: $technology does not support dual index" Loading Loading
launch_universc.sh +48 −8 Original line number Diff line number Diff line Loading @@ -870,9 +870,9 @@ if [[ $setup == "false" ]]; then for j in ${!r1_list[@]}; do read=${r1_list[$j]} R1_file=$read R2_file=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R2/' ) R4_file=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_R4/' ) I1_file=$(echo $indexfile | perl -pne 's/(.*)_R1/$1_I1/' ) R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' ) R4_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R4/' ) I1_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' ) if [[ -f $R4_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fq') ]]; then if [[ $verbose ]]; then echo " file $R4_file found, replacing $R1_file ..." Loading Loading @@ -919,9 +919,49 @@ if [[ $setup == "false" ]]; then #only check I2 for dual-indexed techniques if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq" ]]; then if [[ ${#index2[@]} -ne ${#read1[@]} ]]; then if [[ ${#index2[@]} -gt 0 ]]; then echo " Error: number of index1 files is not matching the number of index2 files" echo " for $technology, either give no index files or give index1 and index2 for each and every read1 and read2 file" exit 1 else if [[ $verbose ]] then echo " No index files given. Automatically detecing from R1 and R2 file names..." fi r1_list=("${read1[@]}") r2_list=("${read2[@]}") i2_list=() for j in ${!r1_list[@]}; do read=${r1_list[$j]} R1_file=$read R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' ) R3_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R3/' ) I2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' ) if [[ -f $R3_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fq') ]]; then if [[ $verbose ]]; then echo " file $R3_file found, replacing $I2_file ..." fi i2_read=$R3_file i2_list[$j]=$i1_read fi if [[ -f $I2_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fq') ]]; then if [[ $verbose ]]; then echo " file $I2_file found..." fi i2_read=$I2_file i2_list[$j]=$i2_read fi done if [ ${#i2_list[@]} -eq 0 ]; then if [[ $verbose ]]; then echo "Dual index files not found" fi else if [ ${#i2_list[@]} -eq 0 ]; then if [[ $verbose ]]; then echo "echo " index files found ${#index2[@]} I2s: ${index2[@]}" fi fi fi fi elif [[ ${#index2[@]} -gt 0 ]]; then echo " Error: $technology does not support dual index" Loading
