From e3a4208284db20fc25828d0ad9c53081b55911de Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 25 Jan 2021 17:30:46 +0100
Subject: [PATCH] samtools: fix filter_bam_mapped
---
src/nf_modules/samtools/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index f1ff8dc8..7e2efd4f 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -30,7 +30,7 @@ process filter_bam_mapped {
tuple val(file_id), path("*_mapped.bam"), emit: bam
script:
"""
-samtools view -@ ${task.cpus} -F 4 -hb ${bam} -L ${bed} > ${file_id}_mapped.bam
+samtools view -@ ${task.cpus} -F 4 -hb ${bam} > ${file_id}_mapped.bam
"""
}
--
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