Loading launch_universc.sh +16 −6 Original line number Diff line number Diff line Loading @@ -319,9 +319,6 @@ for i in {1..2}; do echo "Error: file $read needs a .fq or .fastq extention." exit 1 fi if [[ $verbose == "true" ]]; then echo " $read" fi elif [[ -f $read ]]; then if [[ $read == *"gz" ]]; then gunzip -k $read Loading @@ -332,13 +329,26 @@ for i in {1..2}; do echo "Error: file $read needs a .fq or .fastq extention." exit 1 fi if [[ $verbose == "true" ]]; then echo " $read" fi #allow detection of file extension (needed for --file input) elif [ -f ${read}.fq ] && [ ! -h ${read}.fq ]; then read=${read}.fq elif [ -f ${read}.fastq ] && [ ! -h ${read}.fastq ]; then read=${read}.fastq elif [ -f ${read}.fq.gz ] && [ ! -h ${read}.fq.gz ]l then gunzip -k ${read}.fq.gz read=${read}.fq elif [ -f ${read}.fastq.gz ] && [ ! -h $read ]; then gunzip -k ${read}.fastq.gz read=${read}.fastq else echo "Error: $read not found" exit 1 fi if [[ $verbose == "true" ]]; then echo " $read" fi list[$j]=$read done Loading Loading
launch_universc.sh +16 −6 Original line number Diff line number Diff line Loading @@ -319,9 +319,6 @@ for i in {1..2}; do echo "Error: file $read needs a .fq or .fastq extention." exit 1 fi if [[ $verbose == "true" ]]; then echo " $read" fi elif [[ -f $read ]]; then if [[ $read == *"gz" ]]; then gunzip -k $read Loading @@ -332,13 +329,26 @@ for i in {1..2}; do echo "Error: file $read needs a .fq or .fastq extention." exit 1 fi if [[ $verbose == "true" ]]; then echo " $read" fi #allow detection of file extension (needed for --file input) elif [ -f ${read}.fq ] && [ ! -h ${read}.fq ]; then read=${read}.fq elif [ -f ${read}.fastq ] && [ ! -h ${read}.fastq ]; then read=${read}.fastq elif [ -f ${read}.fq.gz ] && [ ! -h ${read}.fq.gz ]l then gunzip -k ${read}.fq.gz read=${read}.fq elif [ -f ${read}.fastq.gz ] && [ ! -h $read ]; then gunzip -k ${read}.fastq.gz read=${read}.fastq else echo "Error: $read not found" exit 1 fi if [[ $verbose == "true" ]]; then echo " $read" fi list[$j]=$read done Loading
