Loading launch_universc.sh +34 −13 Original line number Diff line number Diff line Loading @@ -9,6 +9,9 @@ if [[ -z $cellrangerpass ]]; then fi ver_info=`paste -d "\n" <(cellranger count --version) <(echo conversion script version 0.1) | head -n 3 | tail -n 2` help="Usage: bash $(basename "$0") -R1=FILE1 -R2=FILE2 -t=TECHNOLOGY -i=ID -r=REFERENCE [--option=OPT] bash $(basename "$0") -R1=READ1_LANE1 READ1_LANE2 -R2=READ2_LANE1 READ2_LANE2 -t=TECHNOLOGY -i=ID -r=REFERENCE [--option=OPT] bash $(basename "$0") -f="SAMPLE_LANE" -t=TECHNOLOGY -i=ID -r=REFERENCE [--option=OPT] bash $(basename "$0") -f="SAMPLE_LANE1" "SAMPLE_LANE2" -t=TECHNOLOGY -i=ID -r=REFERENCE [--option=OPT] bash $(basename "$0") -v bash $(basename "$0") -h bash $(basename "$0") -t=TECHNOLOGY --setup Loading Loading @@ -68,9 +71,7 @@ for op in "$@";do echo "Error: Technology needs to be 10x, nadia, or icell8" exit 1 fi echo "$technology set" shift echo "tech: $@" skip=true fi ;; Loading Loading @@ -138,10 +139,17 @@ for op in "$@";do ;; -f|--file) shift if [[ "$1" != "" ]]; then read1="${1/%\//}_R1_001" read2="${1/%\//}_R2_001" if [[ "$1" != "" ]] then arg=$1 while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]] do echo "file: $arg" read1+="${1/%\//}_R1_001" read2+="${1/%\//}_R2_001" shift arg=$1 done skip=true else echo "Error: File input missing --file or --read1" Loading @@ -168,9 +176,16 @@ for op in "$@";do ;; -R1|--read1) shift if [[ "$1" != "" ]]; then if [[ "$1" != "" ]] then while [[ "$1" != "-"* ]] do if [[ "$1" != "" ]] then read1+=("${1/%\//}") shift fi done skip=true else if [[ -z $read1 ]]; then Loading @@ -181,9 +196,16 @@ for op in "$@";do ;; -R2|--read2) shift if [[ "$1" != "" ]]; then if [[ "$1" != "" ]] then while [[ "$1" != "-"* ]] do if [[ "$1" != "" ]] then read2+=("${1/%\//}") shift fi done skip=true else if [[ -z $read2 ]]; then Loading @@ -197,7 +219,6 @@ for op in "$@";do setup=true skip=false shift echo "setup: $@" ;; --verbose) echo " debugging mode activated" Loading Loading
launch_universc.sh +34 −13 Original line number Diff line number Diff line Loading @@ -9,6 +9,9 @@ if [[ -z $cellrangerpass ]]; then fi ver_info=`paste -d "\n" <(cellranger count --version) <(echo conversion script version 0.1) | head -n 3 | tail -n 2` help="Usage: bash $(basename "$0") -R1=FILE1 -R2=FILE2 -t=TECHNOLOGY -i=ID -r=REFERENCE [--option=OPT] bash $(basename "$0") -R1=READ1_LANE1 READ1_LANE2 -R2=READ2_LANE1 READ2_LANE2 -t=TECHNOLOGY -i=ID -r=REFERENCE [--option=OPT] bash $(basename "$0") -f="SAMPLE_LANE" -t=TECHNOLOGY -i=ID -r=REFERENCE [--option=OPT] bash $(basename "$0") -f="SAMPLE_LANE1" "SAMPLE_LANE2" -t=TECHNOLOGY -i=ID -r=REFERENCE [--option=OPT] bash $(basename "$0") -v bash $(basename "$0") -h bash $(basename "$0") -t=TECHNOLOGY --setup Loading Loading @@ -68,9 +71,7 @@ for op in "$@";do echo "Error: Technology needs to be 10x, nadia, or icell8" exit 1 fi echo "$technology set" shift echo "tech: $@" skip=true fi ;; Loading Loading @@ -138,10 +139,17 @@ for op in "$@";do ;; -f|--file) shift if [[ "$1" != "" ]]; then read1="${1/%\//}_R1_001" read2="${1/%\//}_R2_001" if [[ "$1" != "" ]] then arg=$1 while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]] do echo "file: $arg" read1+="${1/%\//}_R1_001" read2+="${1/%\//}_R2_001" shift arg=$1 done skip=true else echo "Error: File input missing --file or --read1" Loading @@ -168,9 +176,16 @@ for op in "$@";do ;; -R1|--read1) shift if [[ "$1" != "" ]]; then if [[ "$1" != "" ]] then while [[ "$1" != "-"* ]] do if [[ "$1" != "" ]] then read1+=("${1/%\//}") shift fi done skip=true else if [[ -z $read1 ]]; then Loading @@ -181,9 +196,16 @@ for op in "$@";do ;; -R2|--read2) shift if [[ "$1" != "" ]]; then if [[ "$1" != "" ]] then while [[ "$1" != "-"* ]] do if [[ "$1" != "" ]] then read2+=("${1/%\//}") shift fi done skip=true else if [[ -z $read2 ]]; then Loading @@ -197,7 +219,6 @@ for op in "$@";do setup=true skip=false shift echo "setup: $@" ;; --verbose) echo " debugging mode activated" Loading
