Nextflow-ify bash command to extract median read length

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