diff --git a/deep_sequencing_unit/source/bash/cif2txt.sh b/deep_sequencing_unit/source/bash/cif2txt.sh index 7599516f0649abdb9de01954125781a0445b889f..942ffcc7b3f468aab58da8c57091faac536e07ff 100755 --- a/deep_sequencing_unit/source/bash/cif2txt.sh +++ b/deep_sequencing_unit/source/bash/cif2txt.sh @@ -21,13 +21,13 @@ INTENSITY_FOLDER=$1 CYCLES=$2 +NUMBER_OF_TILES=$3 NUMBER_OF_LANES=8 -NUMBER_OF_TILES=100 #INT_NSE_DIR=$1/int_nse PRG=`basename $0` -USAGE="Usage: ${PRG} <Path_to_Intensity_Folder> <Number_of_Cycles> \n\nEXAMPLE: ${PRG} /array0/Runs/090720_42HUDAAXX/Data/Intensities/ 38" +USAGE="Usage: ${PRG} <Path_to_Intensity_Folder> <Number_of_Cycles> \n\nEXAMPLE: ${PRG} /array0/Runs/090720_42HUDAAXX/Data/Intensities/ 38 120" -if [ -z "${INTENSITY_FOLDER}" -o -z "${CYCLES}" ] +if [ -z "${INTENSITY_FOLDER}" -o -z "${CYCLES}" -o -z "${NUMBER_OF_TILES}" ] then echo -e "${USAGE}" exit 1 @@ -41,8 +41,8 @@ for (( l = 1; l <= $NUMBER_OF_LANES; l++ )); do for (( t = 1; t <= $NUMBER_OF_TILES; t++ )); do echo Lane $l Tile $t; # Convert Signal cif to int - /dsf/GAPipeline/bin/cifToTxt -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none + /dsf/GAPipeline/bin/cifToTxt -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none & # Convert Noise cnf to nse (additional -N) - /dsf/GAPipeline/bin/cifToTxt -N -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none + /dsf/GAPipeline/bin/cifToTxt -N -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none & done done