diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index ee012c21fd02ed91ef6d8881bc08805b26397b3f..50e2aef33f7763fe62c5d7b76342bbd952ef09cf 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