From b1330359428f5c43fb300fe46165f0770d55794a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 19 Jan 2020 08:50:55 -0600
Subject: [PATCH] Remove set ends in trimData
---
workflow/rna-seq.nf | 2 --
1 file changed, 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index c0b62d0..802e747 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -189,10 +189,8 @@ process trimData {
# trim fastqs
if [ '${ends_trimData}' == 'se' ]
then
- ends='se'
trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err;
else
- ends='pe'
trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err;
fi
"""
--
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