Loading launch_universc.sh +61 −33 Original line number Diff line number Diff line Loading @@ -536,38 +536,67 @@ if [[ ${#read2[@]} == 1 ]] fi fi echo files: $read1 \(Read1\) and $read2 \(Read2\) unzipR1=$(echo "$read1" | sed 's/\.gz$//') unzipR2=$(echo "$read2" | sed 's/\.gz$//') if [[ -f $read1 ]]; then if [[ $read1 != *'.fastq'* ]] && [[ $read1 != *'.fq'* ]]; then echo "Error: $read1 is not in .fq or .fastq format" exit 1 fi if [[ $read1 == *'.gz' ]]; then echo " unzipping R1 file..." gunzip -kf $read1 fi for i in ${!read1[@]} do read=${read1[$i]} echo " checking file format for $read1 ..." if [ -f $read ] then echo $read elif [ -f ${read}.fq ] then read=${read}.fq echo $read elif [ -f ${read}.fastq ] then read=${read}.fastq echo $read elif [ -f ${read}.fq.gz ] then gunzip -k ${read}.fq.gz read=${read}.fq echo $read elif [ -f ${read}.fastq.gz ] then gunzip -k ${read}.fastq.gz read=${read}.fastq echo $read else echo "Error: $read1 is missing" exit 1 echo $read not found fi read1[$i]=$read done if [[ -f $read2 ]]; then if [[ $read2 != *'.fastq'* ]] && [[ $read2 != *'.fq'* ]]; then echo "Error: $read2 is not in .fq or .fastq format" exit 1 fi if [[ $read2 == *'.gz' ]]; then echo " unzipping R2 file..." gunzip -kf $read2 fi for i in ${!read2[@]} do read=${read2[$i]} echo " checking file format for $read1 ..." if [ -f $read ] then echo $read elif [ -f ${read}.fq ] then read=${read}.fq echo $read elif [ -f ${read}.fastq ] then read=${read}.fastq echo $read elif [ -f ${read}.fq.gz ] then gunzip -k ${read}.fq.gz read=${read}.fq echo $read elif [ -f ${read}.fastq.gz ] then gunzip -k ${read}.fastq.gz read=${read}.fastq echo $read else echo "Error: $read2 is missing" exit 1 echo $read not found fi read2[$i]=$read done echo files: $read1 \(Read1\) and $read2 \(Read2\) Loading @@ -577,11 +606,10 @@ LANE=() for fq in "${read1[@]}"; do name=`basename $fq | cut -f1 -d'.' | grep -o "_" | wc -l | xargs` sn=`basename $fq | cut -f1 -d'_'` ln=`basename $fq | cut -f3 -d'_' | sed 's/L00//'` sn=`basename $fq | cut -f1-$(($name-3)) -d'_'` ln=`basename $fq | cut -f$(($name-1)) -d'_' | sed 's/L00//'` LANE+=($ln) if [[ $name != 4 ]]; then if [[ $name < 4 ]]; then echo "Error: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)"; exit 1 elif [[ $fq != *'.fastq'* ]] && [[ $fq != *'.fq'* ]]; then Loading Loading
launch_universc.sh +61 −33 Original line number Diff line number Diff line Loading @@ -536,38 +536,67 @@ if [[ ${#read2[@]} == 1 ]] fi fi echo files: $read1 \(Read1\) and $read2 \(Read2\) unzipR1=$(echo "$read1" | sed 's/\.gz$//') unzipR2=$(echo "$read2" | sed 's/\.gz$//') if [[ -f $read1 ]]; then if [[ $read1 != *'.fastq'* ]] && [[ $read1 != *'.fq'* ]]; then echo "Error: $read1 is not in .fq or .fastq format" exit 1 fi if [[ $read1 == *'.gz' ]]; then echo " unzipping R1 file..." gunzip -kf $read1 fi for i in ${!read1[@]} do read=${read1[$i]} echo " checking file format for $read1 ..." if [ -f $read ] then echo $read elif [ -f ${read}.fq ] then read=${read}.fq echo $read elif [ -f ${read}.fastq ] then read=${read}.fastq echo $read elif [ -f ${read}.fq.gz ] then gunzip -k ${read}.fq.gz read=${read}.fq echo $read elif [ -f ${read}.fastq.gz ] then gunzip -k ${read}.fastq.gz read=${read}.fastq echo $read else echo "Error: $read1 is missing" exit 1 echo $read not found fi read1[$i]=$read done if [[ -f $read2 ]]; then if [[ $read2 != *'.fastq'* ]] && [[ $read2 != *'.fq'* ]]; then echo "Error: $read2 is not in .fq or .fastq format" exit 1 fi if [[ $read2 == *'.gz' ]]; then echo " unzipping R2 file..." gunzip -kf $read2 fi for i in ${!read2[@]} do read=${read2[$i]} echo " checking file format for $read1 ..." if [ -f $read ] then echo $read elif [ -f ${read}.fq ] then read=${read}.fq echo $read elif [ -f ${read}.fastq ] then read=${read}.fastq echo $read elif [ -f ${read}.fq.gz ] then gunzip -k ${read}.fq.gz read=${read}.fq echo $read elif [ -f ${read}.fastq.gz ] then gunzip -k ${read}.fastq.gz read=${read}.fastq echo $read else echo "Error: $read2 is missing" exit 1 echo $read not found fi read2[$i]=$read done echo files: $read1 \(Read1\) and $read2 \(Read2\) Loading @@ -577,11 +606,10 @@ LANE=() for fq in "${read1[@]}"; do name=`basename $fq | cut -f1 -d'.' | grep -o "_" | wc -l | xargs` sn=`basename $fq | cut -f1 -d'_'` ln=`basename $fq | cut -f3 -d'_' | sed 's/L00//'` sn=`basename $fq | cut -f1-$(($name-3)) -d'_'` ln=`basename $fq | cut -f$(($name-1)) -d'_' | sed 's/L00//'` LANE+=($ln) if [[ $name != 4 ]]; then if [[ $name < 4 ]]; then echo "Error: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)"; exit 1 elif [[ $fq != *'.fastq'* ]] && [[ $fq != *'.fq'* ]]; then Loading
