From 449693e29ec064b505752c97f571fca7c86d8b72 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 25 Feb 2021 09:59:29 +0100
Subject: [PATCH] bwa: add params.bwa_mem_R variable
---
src/nf_modules/bwa/main.nf | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 8f395a60..42cd6077 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -21,6 +21,7 @@ bwa index -p ${fasta.simpleName} ${fasta} \
}
+params.bwa_mem_R = '@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina'
process mapping_fastq {
container = "${container_url}"
label "big_mem_multi_cpus"
@@ -37,6 +38,7 @@ process mapping_fastq {
script:
"""
bwa mem -t ${task.cpus} \
+-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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