From f99bfd2adf12d74328eec812c225646f2bfa3c0f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 3 Aug 2020 22:19:21 -0500
Subject: [PATCH] Fix measure read length
---
workflow/rna-seq.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index f98ffa7..29107b6 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
--
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