From 97953ba25f6cf2392aebd1772d56579ab6c6a08d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 25 Feb 2021 10:13:07 +0100
Subject: [PATCH] bwa: add quote surrounding -R option
---
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 67ab9227..d422ca0a 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -38,7 +38,7 @@ process mapping_fastq {
script:
"""
bwa mem -t ${task.cpus} \
--R ${params.bwa_mem_R} \
+-R '${params.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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