From 86b3d5ab97ac4cb04b7e32d262aa958d5623a2e2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 3 May 2021 10:55:55 +0200
Subject: [PATCH] bwa: fix index names in mapping
---
src/nf_modules/bwa/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 39ee8157..1e4da4bd 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -66,7 +66,7 @@ bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumi
bwa mem -t ${task.cpus} \
${params.mapping_fastq} \
-R '${bwa_mem_R}' \
-${index.baseName} ${reads[0]} ${reads[1]} 2> \
+${index[0].baseName} ${reads[0]} ${reads[1]} 2> \
${file_prefix}_bwa_report.txt | \
samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
"""
@@ -75,7 +75,7 @@ ${index.baseName} ${reads[0]} ${reads[1]} 2> \
bwa mem -t ${task.cpus} \
${params.mapping_fastq} \
-R '${bwa_mem_R}' \
-${index.baseName} ${reads} 2> \
+${index[0].baseName} ${reads} 2> \
${file_prefix}_bwa_report.txt | \
samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
"""
--
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