Loading launch_universc.sh +23 −5 Original line number Diff line number Diff line Loading @@ -1136,8 +1136,8 @@ if [[ $setup == "false" ]]; then if [[ $verbose ]]; then echo " file $R3_file found, replacing $I2_file ..." fi i2_read=$R3_file i2_list[$j]=$i1_read r3_read=$R3_file i2_list[$j]=$r3_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 i2_present="true" Loading Loading @@ -1184,9 +1184,11 @@ fi keys=("R1" "R2") if [[ $r3_present == "true" ]]; then keys=(${keys[@]} "R3") read3=("${index2[@]}") fi if [[ $r4_present == "true" ]]; then keys=(${keys[@]} "R4") read4=("${index1[@]}") fi if [[ $i1_present == "true" ]]; then keys=(${keys[@]} "I1") Loading @@ -1201,7 +1203,7 @@ fi #####Input file curation 2: Check R1, R2, I1, and I2 files for their extensions##### ##allows incomplete file names and processing compressed files if [[ $verbose ]]; then echo "key: ${keys[@]}" echo "keys: ${keys[@]}" fi for key in ${keys[@]}; do if [[ $verbose ]]; then Loading Loading @@ -1497,6 +1499,12 @@ if [[ $verbose ]]; then echo " Input files post-curation 3" echo " ${#read1[@]}files - read1s: ${read1[@]}" echo " ${#read2[@]}files - read2s: ${read2[@]}" if [[ ${#read3[@]} -gt 0 ]]; then echo " ${#read3[@]}files - R3s: ${read3[@]}" fi if [[ ${#read4[@]} -gt 0 ]]; then echo " ${#read4[@]}files - R4s: ${read4[@]}" fi if [[ ${#index1[@]} -gt 0 ]]; then echo " ${#index1[@]}files - I1s: ${index1[@]}" fi Loading Loading @@ -1673,6 +1681,12 @@ if [[ $verbose ]]; then echo " Input files post-curation 4" echo " ${#read1[@]}files - read1s: ${read1[@]}" echo " ${#read2[@]}files - read2s: ${read2[@]}" if [[ ${#read3[@]} -gt 0 ]]; then echo " ${#read3[@]}files - R3s: ${read3[@]}" fi if [[ ${#read4[@]} -gt 0 ]]; then echo " ${#read4[@]}files - R4s: ${read4[@]}" fi if [[ ${#index1[@]} -gt 0 ]]; then echo " ${#index1[@]}files - I1s: ${index1[@]}" fi Loading @@ -1688,7 +1702,11 @@ fi #####Input file curation 5: Catpuring sample name##### #checking the quality of fastq file names read12=("${read1[@]}" "${read2[@]}") if [[ ${#index2[@]} -gt 0 ]]; then if [[ ${#read3[@]} -gt 0 ]] && [[ ${#read4[@]} -gt 0 ]]; then read12=("${read1[@]}" "${read2[@]}" "${read3[@]}" "${read4[@]}") elif [[ ${#index1[@]} -gt 0 ]] && [[ ${#read3[@]} -gt 0 ]]; then read12=("${read1[@]}" "${read2[@]}" "${read3[@]}" "${index1[@]}") elif [[ ${#index2[@]} -gt 0 ]]; then read12=("${read1[@]}" "${read2[@]}" "${index1[@]}" "${index2[@]}") elif [[ ${#index1[@]} -gt 0 ]]; then read12=("${read1[@]}" "${read2[@]}" "${index1[@]}") Loading Loading
launch_universc.sh +23 −5 Original line number Diff line number Diff line Loading @@ -1136,8 +1136,8 @@ if [[ $setup == "false" ]]; then if [[ $verbose ]]; then echo " file $R3_file found, replacing $I2_file ..." fi i2_read=$R3_file i2_list[$j]=$i1_read r3_read=$R3_file i2_list[$j]=$r3_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 i2_present="true" Loading Loading @@ -1184,9 +1184,11 @@ fi keys=("R1" "R2") if [[ $r3_present == "true" ]]; then keys=(${keys[@]} "R3") read3=("${index2[@]}") fi if [[ $r4_present == "true" ]]; then keys=(${keys[@]} "R4") read4=("${index1[@]}") fi if [[ $i1_present == "true" ]]; then keys=(${keys[@]} "I1") Loading @@ -1201,7 +1203,7 @@ fi #####Input file curation 2: Check R1, R2, I1, and I2 files for their extensions##### ##allows incomplete file names and processing compressed files if [[ $verbose ]]; then echo "key: ${keys[@]}" echo "keys: ${keys[@]}" fi for key in ${keys[@]}; do if [[ $verbose ]]; then Loading Loading @@ -1497,6 +1499,12 @@ if [[ $verbose ]]; then echo " Input files post-curation 3" echo " ${#read1[@]}files - read1s: ${read1[@]}" echo " ${#read2[@]}files - read2s: ${read2[@]}" if [[ ${#read3[@]} -gt 0 ]]; then echo " ${#read3[@]}files - R3s: ${read3[@]}" fi if [[ ${#read4[@]} -gt 0 ]]; then echo " ${#read4[@]}files - R4s: ${read4[@]}" fi if [[ ${#index1[@]} -gt 0 ]]; then echo " ${#index1[@]}files - I1s: ${index1[@]}" fi Loading Loading @@ -1673,6 +1681,12 @@ if [[ $verbose ]]; then echo " Input files post-curation 4" echo " ${#read1[@]}files - read1s: ${read1[@]}" echo " ${#read2[@]}files - read2s: ${read2[@]}" if [[ ${#read3[@]} -gt 0 ]]; then echo " ${#read3[@]}files - R3s: ${read3[@]}" fi if [[ ${#read4[@]} -gt 0 ]]; then echo " ${#read4[@]}files - R4s: ${read4[@]}" fi if [[ ${#index1[@]} -gt 0 ]]; then echo " ${#index1[@]}files - I1s: ${index1[@]}" fi Loading @@ -1688,7 +1702,11 @@ fi #####Input file curation 5: Catpuring sample name##### #checking the quality of fastq file names read12=("${read1[@]}" "${read2[@]}") if [[ ${#index2[@]} -gt 0 ]]; then if [[ ${#read3[@]} -gt 0 ]] && [[ ${#read4[@]} -gt 0 ]]; then read12=("${read1[@]}" "${read2[@]}" "${read3[@]}" "${read4[@]}") elif [[ ${#index1[@]} -gt 0 ]] && [[ ${#read3[@]} -gt 0 ]]; then read12=("${read1[@]}" "${read2[@]}" "${read3[@]}" "${index1[@]}") elif [[ ${#index2[@]} -gt 0 ]]; then read12=("${read1[@]}" "${read2[@]}" "${index1[@]}" "${index2[@]}") elif [[ ${#index1[@]} -gt 0 ]]; then read12=("${read1[@]}" "${read2[@]}" "${index1[@]}") Loading
