From e801efee116c9a80a4c5bde35326d04095aaa8c0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 14:40:09 +0100
Subject: [PATCH] bwa: fix previous commit
---
src/nf_modules/bwa/main.nf | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index c485f75d..785201c7 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -35,10 +35,11 @@ process mapping_fastq {
tuple val(file_id), path("${file_id}_bwa_report.txt"), emit: report
script:
-if (file_id.containsKey('library')):
+if (file_id.containsKey('library')) {
library = file_id.library
-else:
+} else {
library = file_id
+}
bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
"""
bwa mem -t ${task.cpus} \
--
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