From 493aaa150e4c7135cd6f80ae522dfb3688d1c7d0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 22 Feb 2021 12:16:40 +0100
Subject: [PATCH] samtools: fix merge_multi_bam
---
src/nf_modules/samtools/main.nf | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 75bbb514..d778e31f 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -178,8 +178,10 @@ process merge_multi_bam {
tuple val(file_id), path("*_merged.bam*"), emit: bam
script:
"""
-samtools merge ${bams} > \
- ${bams[0].simpleName}_merged.bam
+samtools merge -@ ${task.cpus} \
+ ${bams[0].simpleName}_merged.bam \
+ ${bams}
+
"""
}
--
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