Loading launch_universc.sh +36 −7 Original line number Diff line number Diff line Loading @@ -912,12 +912,16 @@ if [[ "$technology" == "indrop-v3" ]]; then fi fi if [[ $verbose = "true" ]]; then if [[ $verbose ]]; then echo "${#read1[@]} read1s: ${read1[@]}" echo "${#read2[@]} read2s: ${read2[@]}" if [[ ${#index1[@]} -ge 1 ]]; then echo "${#index1[@]} I1s: ${index1[@]}" fi if [[ ${#index2[@]} -ge 1 ]]; then echo "${#index2[@]} I2s: ${index2[@]}" fi fi #check number of index1 files is 0 or number of read1 files if [[ ${#index1[@]} -eq ${#read1[@]} ]] || [[ ${#index1[@]} -eq 0 ]]; then Loading @@ -926,8 +930,10 @@ if [[ ${#index1[@]} -eq ${#read1[@]} ]] || [[ ${#index1[@]} -eq 0 ]]; then keys=("R1" "R2" "I1") fi if [[ ${#index1[@]} -eq 0 ]]; then if [[ $verbose ]]; then echo "... index1 files not found (optional)" fi fi else echo "... index1 files missing for some samples or lanes (will be skipped)" index1=() Loading @@ -938,8 +944,10 @@ if [[ ${#index1[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -eq ${#read1[@]} ]] keys=("R1" "R2" "I1" "I2") fi if [[ ${#index2[@]} -eq 0 ]]; then if [[ $verbose ]]; then echo "... index2 files not found (optional)" fi fi else echo "... index2 files missing for some samples or lanes (will be skipped)" index2=() Loading @@ -948,6 +956,9 @@ fi #check read1 and read2 files for their extensions ##allows incomplete file names and processing compressed files if [[ $verbose ]]; then echo "key: ${keys[@]}" fi for key in ${keys[@]}; do readkey=$key list="" Loading Loading @@ -1020,9 +1031,16 @@ for key in ${keys[@]}; do fi done if [[ $verbose ]]; then echo "key: ${keys[@]}" fi #renaming read1 and read2 files if not compatible with the convention for i in ${keys[@]}; do for key in ${keys[@]}; do readkey=$key if [[ $verbose ]]; then echo $readkey here fi list="" if [[ $readkey == "R1" ]]; then list=("${read1[@]}") Loading Loading @@ -1138,7 +1156,13 @@ if [[ ${#index1[@]} -ge 1 ]]; then read12=("${read1[@]}" "${read2[@]}" "${index1[@]}" "${index2[@]}") fi fi if [[ $verbose == true ]]; then echo "reads:" ${read12[@]} fi for fq in "${read12[@]}"; do if [[ $verbose ]]; then echo "read: $fq" fi name=`basename $fq` name=${name%.*} fields=`echo ${name} | grep -o "_" | wc -l` Loading @@ -1157,6 +1181,11 @@ for fq in "${read12[@]}"; do exit 1 fi if [[ $verbose == true ]]; then echo "SAMPLE: $SAMPLE" echo "sample (field): $sn" fi if [[ ${sn} != $SAMPLE ]]; then if [[ -z $SAMPLE ]]; then SAMPLE=${sn} Loading Loading
launch_universc.sh +36 −7 Original line number Diff line number Diff line Loading @@ -912,12 +912,16 @@ if [[ "$technology" == "indrop-v3" ]]; then fi fi if [[ $verbose = "true" ]]; then if [[ $verbose ]]; then echo "${#read1[@]} read1s: ${read1[@]}" echo "${#read2[@]} read2s: ${read2[@]}" if [[ ${#index1[@]} -ge 1 ]]; then echo "${#index1[@]} I1s: ${index1[@]}" fi if [[ ${#index2[@]} -ge 1 ]]; then echo "${#index2[@]} I2s: ${index2[@]}" fi fi #check number of index1 files is 0 or number of read1 files if [[ ${#index1[@]} -eq ${#read1[@]} ]] || [[ ${#index1[@]} -eq 0 ]]; then Loading @@ -926,8 +930,10 @@ if [[ ${#index1[@]} -eq ${#read1[@]} ]] || [[ ${#index1[@]} -eq 0 ]]; then keys=("R1" "R2" "I1") fi if [[ ${#index1[@]} -eq 0 ]]; then if [[ $verbose ]]; then echo "... index1 files not found (optional)" fi fi else echo "... index1 files missing for some samples or lanes (will be skipped)" index1=() Loading @@ -938,8 +944,10 @@ if [[ ${#index1[@]} -eq ${#read1[@]} ]] && [[ ${#index2[@]} -eq ${#read1[@]} ]] keys=("R1" "R2" "I1" "I2") fi if [[ ${#index2[@]} -eq 0 ]]; then if [[ $verbose ]]; then echo "... index2 files not found (optional)" fi fi else echo "... index2 files missing for some samples or lanes (will be skipped)" index2=() Loading @@ -948,6 +956,9 @@ fi #check read1 and read2 files for their extensions ##allows incomplete file names and processing compressed files if [[ $verbose ]]; then echo "key: ${keys[@]}" fi for key in ${keys[@]}; do readkey=$key list="" Loading Loading @@ -1020,9 +1031,16 @@ for key in ${keys[@]}; do fi done if [[ $verbose ]]; then echo "key: ${keys[@]}" fi #renaming read1 and read2 files if not compatible with the convention for i in ${keys[@]}; do for key in ${keys[@]}; do readkey=$key if [[ $verbose ]]; then echo $readkey here fi list="" if [[ $readkey == "R1" ]]; then list=("${read1[@]}") Loading Loading @@ -1138,7 +1156,13 @@ if [[ ${#index1[@]} -ge 1 ]]; then read12=("${read1[@]}" "${read2[@]}" "${index1[@]}" "${index2[@]}") fi fi if [[ $verbose == true ]]; then echo "reads:" ${read12[@]} fi for fq in "${read12[@]}"; do if [[ $verbose ]]; then echo "read: $fq" fi name=`basename $fq` name=${name%.*} fields=`echo ${name} | grep -o "_" | wc -l` Loading @@ -1157,6 +1181,11 @@ for fq in "${read12[@]}"; do exit 1 fi if [[ $verbose == true ]]; then echo "SAMPLE: $SAMPLE" echo "sample (field): $sn" fi if [[ ${sn} != $SAMPLE ]]; then if [[ -z $SAMPLE ]]; then SAMPLE=${sn} Loading
