From e7bfb733cdbe76cc07ef9c272d644a8f0db1b283 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Sat, 20 Feb 2021 08:31:54 +0100
Subject: [PATCH] bwa: fix typo :42

---
 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 a6b60adc..e97f218a 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -39,7 +39,7 @@ process mapping_fastq {
 bwa mem -t ${task.cpus} \
 ${index_id} ${reads[0]} ${reads[1]} 2> \
   ${file_id}_bwa_report.txt | \
-  samtools view -@ ${task.cpus} -Sb - > ${pair_id}.bam
+  samtools view -@ ${task.cpus} -Sb - > ${file_id}.bam
 """
 }
 
-- 
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