From 18e214ae52edb640a2aee490e8172e69a7133c5a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Apr 2021 17:27:33 +0200
Subject: [PATCH] cutadapt: fix bug :28
---
src/nf_modules/cutadapt/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/cutadapt/main.nf b/src/nf_modules/cutadapt/main.nf
index 7b459f81..a4d08fe8 100644
--- a/src/nf_modules/cutadapt/main.nf
+++ b/src/nf_modules/cutadapt/main.nf
@@ -19,13 +19,13 @@ 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 \
--
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