From c99e5a39eef82b84b31c1b71f36a06b760b36749 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Sat, 20 Feb 2021 08:24:24 +0100
Subject: [PATCH] bwa: fix typo :42
---
src/nf_modules/bwa/main.nf | 1 -
1 file changed, 1 deletion(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index ada553fe..a6b60adc 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -39,7 +39,6 @@ process mapping_fastq {
bwa mem -t ${task.cpus} \
${index_id} ${reads[0]} ${reads[1]} 2> \
${file_id}_bwa_report.txt | \
- samtools view -S -t ${task.cpus} -f bam - > ${file_id}.bam
samtools view -@ ${task.cpus} -Sb - > ${pair_id}.bam
"""
}
--
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