From 801d4f6a982dc8b5e18991b38188f545d3cf233c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 14:41:21 +0100
Subject: [PATCH] bwa: fix bug :46
---
src/nf_modules/bwa/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 785201c7..7d2abd12 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -43,7 +43,7 @@ if (file_id.containsKey('library')) {
bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
"""
bwa mem -t ${task.cpus} \
--R '${params.bwa_mem_R}' \
+-R '${bwa_mem_R}' \
${index_id} ${reads[0]} ${reads[1]} 2> \
${file_id}_bwa_report.txt | \
samtools view -@ ${task.cpus} -Sb - > ${file_id}.bam
--
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