From a4d4bdb968e7538c0c075573653cea3ad583f953 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 29 Jan 2021 11:08:44 +0100
Subject: [PATCH] samtools: add bam_stats process
---
src/nf_modules/samtools/main.nf | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 7e2efd4f..4f197fbd 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -123,3 +123,20 @@ process merge_bam {
samtools merge ${first_bam} ${second_bam} ${first_bam_id}_${second_file_id}.bam
"""
}
+
+process bam_stats {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+ cpus = 2
+
+ input:
+ tuple val(file_id), path(bam)
+
+ output:
+ tuple val(file_id), path("*.tsv"), emit: tsv
+ script:
+"""
+samtools flagstat -O tsv ${bam} > ${file_id}.tsv
+"""
+}
--
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