diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index f98ffa791ed26cf724892046e21a934208bb17ac..29107b65d7203bbee5235e17d086dc72275e9507 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -307,7 +307,7 @@ process trimData { 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