diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 3e7e3aa13e7497fbd5e94dfa5e9f365a550f5434..57f3e9aad9deccd696ebdd15e18c6a612df29193 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -299,11 +299,11 @@ process trimData { if [ "${ends}" == "se" ] then trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]} - readLength=\$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length(\${1})}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}') + readLength=\$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length(\${1})}' | sort -n | awk '{a[NR]=\$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}') elif [ "${ends}" == "pe" ] then trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]} - readLength=\$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length(\${1})}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}') + readLength=\$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length(\${1})}' | sort -n | awk '{a[NR]=\$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}') fi echo -e "LOG: trimmed" >> ${repRID}.trimData.log echo -e "LOG: average trimmed read length: \${readLength}" >> ${repRID}.trimData.log @@ -317,7 +317,7 @@ process trimData { readLengthInfer = Channel.create() inferMetadata_readLength.splitCsv(sep: ",", header: false).separate( readLengthInfer -} +) // Replicate trimmed fastq's