From 0db3382ce1ab3655696db6866b6b5f19d4025505 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 11:29:14 +0100
Subject: [PATCH] bwa: fix bam tag format
---
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 d422ca0a..f93b91e2 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -21,7 +21,6 @@ bwa index -p ${fasta.simpleName} ${fasta} \
}
-params.bwa_mem_R = '@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina'
process mapping_fastq {
container = "${container_url}"
label "big_mem_multi_cpus"
@@ -36,6 +35,7 @@ process mapping_fastq {
tuple val(file_id), path("${file_id}_bwa_report.txt"), emit: report
script:
+bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
"""
bwa mem -t ${task.cpus} \
-R '${params.bwa_mem_R}' \
--
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