From d69ff6ea472972dc649bc662cec63bef8f7bc17e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Apr 2021 17:29:28 +0200
Subject: [PATCH] cutadapt: fix typo :34
---
src/nf_modules/cutadapt/main.nf | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/cutadapt/main.nf b/src/nf_modules/cutadapt/main.nf
index a4d08fe8..3307dd40 100644
--- a/src/nf_modules/cutadapt/main.nf
+++ b/src/nf_modules/cutadapt/main.nf
@@ -19,18 +19,19 @@ process adaptor_removal {
path "*_report.txt", emit: report
script:
-if (reads instanceof List) {
+ if (reads instanceof List) {
"""
cutadapt ${params.adaptor_removal} \
-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
-} else {
+ } else {
"""
cutadapt ${params.adaptor_removal} \
-o ${file_id}_cut.fastq.gz \
${reads} > ${file_id}_report.txt
"""
+ }
}
params.adaptor_removal_pairedend = "-a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim}"
--
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