Loading launch_universc.sh +37 −2 Original line number Diff line number Diff line Loading @@ -34,6 +34,8 @@ Mandatory arguments to long options are mandatory for short options too. -h, --help Display this help and exit -v, --version Output version information and exit -s, --setup Set up whitelists for compatibility with new technology -k, --keep Keep converted files -x, --skip Skip conversion and run cellranger --verbose Print additional outputs for debugging For each fastq file, follow the following naming convention: Loading @@ -52,6 +54,8 @@ fi #reading in options read1=() read2=() keep=false convert=true skip=false for op in "$@";do if $skip;then skip=false;continue;fi Loading Loading @@ -225,6 +229,19 @@ for op in "$@";do skip=false shift ;; -k|--keep) echo " converted files will be kept if already exists" keep=true skip=false shift ;; -x|--skip) echo " running ${cellrangerpass} on existing converted files" keep=true convert=false skip=false shift ;; --verbose) echo " debugging mode activated" verbose=true Loading Loading @@ -708,6 +725,12 @@ LANE=$(echo "${LANE[@]}" | tr ' ' '\n' | sort -u | tr '\n' ',' | sed 's/,$//') #create directory of modified files echo " creating a folder for all cellranger input files..." crIN="cellranger" if [ ! $crIN ] then echo " directory $crIN created for converted files" else echo " directory $crIN already exists" fi mkdir -p $crIN if [ -d $crIN ] then Loading @@ -718,7 +741,13 @@ if [ -d $crIN ] then echo "warning: converted $read file already exists" fi if [ ! keep ] then echo "file $crIN/$read removed" rm -rf $crIN/$read else echo "file $crIN/$read kept" fi done for i in ${!read2[@]} do Loading @@ -727,7 +756,13 @@ if [ -d $crIN ] then echo "warning: converted $read file already exists" fi if [ ! keep ] then echo "file $crIN/$read removed" rm -rf $crIN/$read else echo "file $crIN/$read kept" fi done fi Loading Loading
launch_universc.sh +37 −2 Original line number Diff line number Diff line Loading @@ -34,6 +34,8 @@ Mandatory arguments to long options are mandatory for short options too. -h, --help Display this help and exit -v, --version Output version information and exit -s, --setup Set up whitelists for compatibility with new technology -k, --keep Keep converted files -x, --skip Skip conversion and run cellranger --verbose Print additional outputs for debugging For each fastq file, follow the following naming convention: Loading @@ -52,6 +54,8 @@ fi #reading in options read1=() read2=() keep=false convert=true skip=false for op in "$@";do if $skip;then skip=false;continue;fi Loading Loading @@ -225,6 +229,19 @@ for op in "$@";do skip=false shift ;; -k|--keep) echo " converted files will be kept if already exists" keep=true skip=false shift ;; -x|--skip) echo " running ${cellrangerpass} on existing converted files" keep=true convert=false skip=false shift ;; --verbose) echo " debugging mode activated" verbose=true Loading Loading @@ -708,6 +725,12 @@ LANE=$(echo "${LANE[@]}" | tr ' ' '\n' | sort -u | tr '\n' ',' | sed 's/,$//') #create directory of modified files echo " creating a folder for all cellranger input files..." crIN="cellranger" if [ ! $crIN ] then echo " directory $crIN created for converted files" else echo " directory $crIN already exists" fi mkdir -p $crIN if [ -d $crIN ] then Loading @@ -718,7 +741,13 @@ if [ -d $crIN ] then echo "warning: converted $read file already exists" fi if [ ! keep ] then echo "file $crIN/$read removed" rm -rf $crIN/$read else echo "file $crIN/$read kept" fi done for i in ${!read2[@]} do Loading @@ -727,7 +756,13 @@ if [ -d $crIN ] then echo "warning: converted $read file already exists" fi if [ ! keep ] then echo "file $crIN/$read removed" rm -rf $crIN/$read else echo "file $crIN/$read kept" fi done fi Loading
