From 70a181f4a1ce00cfff91ea2468a206c53d0099d1 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 14:38:45 +0100
Subject: [PATCH] bwa: conditional definition of the library tag
---
src/nf_modules/bwa/main.nf | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index f93b91e2..c485f75d 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -35,6 +35,10 @@ process mapping_fastq {
tuple val(file_id), path("${file_id}_bwa_report.txt"), emit: report
script:
+if (file_id.containsKey('library')):
+ library = file_id.library
+else:
+ library = file_id
bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
"""
bwa mem -t ${task.cpus} \
--
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