Loading CPU/juicer.sh +8 −9 Original line number Diff line number Diff line Loading @@ -249,6 +249,14 @@ if [[ -z "$final" && -z "$dedup" && -z "$postproc" && -z "$deduponly" && -z "$me if stat -t ${fastqdir} >/dev/null 2>&1 then echo "(-: Looking for fastq files...fastq files exist" testname=$(ls -l ${fastqdir} | awk 'NR==1{print $9}') if [ "${testname: -3}" == ".gz" ] then read1=${splitdir}"/*${read1str}*.fastq.gz" gzipped=1 else read1=${splitdir}"/*${read1str}*.fastq" fi else if [ ! -d "$splitdir" ]; then echo "***! Failed to find any files matching ${fastqdir}" Loading Loading @@ -287,15 +295,6 @@ fi ## Arguments have been checked and directories created. Now begins ## the real work of the pipeline testname=$(ls -l ${fastqdir} | awk 'NR==1{print $9}') if [ "${testname: -3}" == ".gz" ] then read1=${splitdir}"/*${read1str}*.fastq.gz" gzipped=1 else read1=${splitdir}"/*${read1str}*.fastq" fi headfile=${outputdir}/header date > $headfile # Experiment description Loading Loading
CPU/juicer.sh +8 −9 Original line number Diff line number Diff line Loading @@ -249,6 +249,14 @@ if [[ -z "$final" && -z "$dedup" && -z "$postproc" && -z "$deduponly" && -z "$me if stat -t ${fastqdir} >/dev/null 2>&1 then echo "(-: Looking for fastq files...fastq files exist" testname=$(ls -l ${fastqdir} | awk 'NR==1{print $9}') if [ "${testname: -3}" == ".gz" ] then read1=${splitdir}"/*${read1str}*.fastq.gz" gzipped=1 else read1=${splitdir}"/*${read1str}*.fastq" fi else if [ ! -d "$splitdir" ]; then echo "***! Failed to find any files matching ${fastqdir}" Loading Loading @@ -287,15 +295,6 @@ fi ## Arguments have been checked and directories created. Now begins ## the real work of the pipeline testname=$(ls -l ${fastqdir} | awk 'NR==1{print $9}') if [ "${testname: -3}" == ".gz" ] then read1=${splitdir}"/*${read1str}*.fastq.gz" gzipped=1 else read1=${splitdir}"/*${read1str}*.fastq" fi headfile=${outputdir}/header date > $headfile # Experiment description Loading
