From aa8386656a41e1b5f63bcdfb7b6af9cce8128a51 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 22 Feb 2021 12:10:28 +0100
Subject: [PATCH] samtools: fix merge_multi_bam
---
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 9493c0e4..75bbb514 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -178,7 +178,7 @@ process merge_multi_bam {
tuple val(file_id), path("*_merged.bam*"), emit: bam
script:
"""
-samtools merge ${bams} \
+samtools merge ${bams} > \
${bams[0].simpleName}_merged.bam
"""
}
--
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