From 1f25c4c5c3615e919c1fda528d26f2458e96b7b6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 26 Apr 2021 17:29:48 +0200
Subject: [PATCH] samtools: fix split_bam @ option
---
src/nf_modules/samtools/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 208540dd..4d5c9313 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -174,9 +174,9 @@ process split_bam {
tuple val(file_id), path("*_reverse.bam*"), emit: bam_reverse
script:
"""
-samtools view --@ ${Math.round(task.cpus/2)} ${params.split_bam} \
+samtools view -@ ${Math.round(task.cpus/2)} ${params.split_bam} \
-hb -F 0x10 ${bam} > ${bam.simpleName}_forward.bam &
-samtools view --@ ${Math.round(task.cpus/2)} ${params.split_bam} \
+samtools view -@ ${Math.round(task.cpus/2)} ${params.split_bam} \
-hb -f 0x10 ${bam} > ${bam.simpleName}_reverse.bam
"""
}
--
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