Loading launch_universc.sh +29 −19 Original line number Diff line number Diff line Loading @@ -775,15 +775,6 @@ if [[ ${#index1[@]} -eq ${#read1[@]} ]] && [[ ${#index1[@]} -ge 1 ]]; then echo "WARNING: mismatch in number of files (check index I1 files)" echo "NOTE: if no index files are specified, these can be detected from R1 file names" fi elif [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then if [[ ${#index2[@]} -eq 1 ]]; then echo " index2 $index2 passes" elif [[ ${#index2[@]} -ge 2 ]]; then echo " indices $index2 passes" else echo "WARNING: mismatch in number of files (check index I2 files)" echo "NOTE: if no index files are specified, these can be detected from R1 file names" fi else #if number of files mismatch or no index1 given echo " checking for index1 files..." Loading @@ -796,6 +787,9 @@ else if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then index1+=("$indexfile") fi done fi #check for dual indexing (I2 files) #####check dual index(I1 and I2)##### ## Note that indexes are copied ## Loading @@ -803,17 +797,33 @@ else ## Demultiplex with bcl2fastq ## ## This is a work-in-progress ## ##################################### # 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 1 ]]; then echo " index2 $index2 passes" elif [[ ${#index2[@]} -ge 2 ]]; then echo " indices $index2 passes" else echo "WARNING: mismatch in number of files (check index I2 files)" echo "NOTE: if no index files are specified, these can be detected from R1 file names" fi else #if number of files mismatch or no index1 given echo " checking for index1 files..." for ii in $(seq 1 1 ${#read1[@]}); do #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I2 filename for R1 filename indexfile=$(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 ${indexfile}.fq.gz ]]; then index2+=("$indexfile") fi fi done fi fi if [[ $verbose = "true" ]]; then echo "${#read1[@]} read1s: ${read1[@]}" Loading Loading
launch_universc.sh +29 −19 Original line number Diff line number Diff line Loading @@ -775,15 +775,6 @@ if [[ ${#index1[@]} -eq ${#read1[@]} ]] && [[ ${#index1[@]} -ge 1 ]]; then echo "WARNING: mismatch in number of files (check index I1 files)" echo "NOTE: if no index files are specified, these can be detected from R1 file names" fi elif [[ ${#index2[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -ge 1 ]]; then if [[ ${#index2[@]} -eq 1 ]]; then echo " index2 $index2 passes" elif [[ ${#index2[@]} -ge 2 ]]; then echo " indices $index2 passes" else echo "WARNING: mismatch in number of files (check index I2 files)" echo "NOTE: if no index files are specified, these can be detected from R1 file names" fi else #if number of files mismatch or no index1 given echo " checking for index1 files..." Loading @@ -796,6 +787,9 @@ else if [[ -f $indexfile ]] || [[ -f ${indexfile}.gz ]] || [[ -f $indexfile.fastq ]] || [[ -f ${indexfile}.fastq.gz ]] || [[ -f $indexfile.fq ]] || [[ -f ${indexfile}.fq.gz ]]; then index1+=("$indexfile") fi done fi #check for dual indexing (I2 files) #####check dual index(I1 and I2)##### ## Note that indexes are copied ## Loading @@ -803,17 +797,33 @@ else ## Demultiplex with bcl2fastq ## ## This is a work-in-progress ## ##################################### # 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 1 ]]; then echo " index2 $index2 passes" elif [[ ${#index2[@]} -ge 2 ]]; then echo " indices $index2 passes" else echo "WARNING: mismatch in number of files (check index I2 files)" echo "NOTE: if no index files are specified, these can be detected from R1 file names" fi else #if number of files mismatch or no index1 given echo " checking for index1 files..." for ii in $(seq 1 1 ${#read1[@]}); do #iterate over read1 inputs indexfile=${read1[$(( $ii -1 ))]} #derive I2 filename for R1 filename indexfile=$(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 ${indexfile}.fq.gz ]]; then index2+=("$indexfile") fi fi done fi fi if [[ $verbose = "true" ]]; then echo "${#read1[@]} read1s: ${read1[@]}" Loading
