From ff5c7a24d9815c4a304407ee541f72ee27cb01ec Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 17 Feb 2021 10:00:03 +0100
Subject: [PATCH] samtools: add process to merge multiple bam
---
src/nf_modules/samtools/main.nf | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 20db864f..7af44dda 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -165,6 +165,24 @@ samtools merge ${first_bam} ${second_bam} \
"""
}
+process merge_multi_bam {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+ cpus = 2
+
+ input:
+ tuple val(file_id), path(bams)
+
+ output:
+ tuple val(file_id), path("*.bam*"), emit: bam
+ script:
+"""
+samtools merge ${bams} \
+ ${file_id}.bam
+"""
+}
+
process stats_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
--
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