From ef37d9830cf65b1c48746624cacd2727dd8281ba Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 4 Feb 2021 10:19:34 +0100
Subject: [PATCH] nf_modules: add bam to bedgraph and change deeptools version
---
src/nf_modules/bedtools/main.nf | 19 +++++++++++++++++++
src/nf_modules/deeptools/main.nf | 2 +-
2 files changed, 20 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index f0bef131..616435bc 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -55,3 +55,22 @@ bedtools bamtofastq \
-i ${bam} -fq ${bam.baseName}_R1.fastq -fq2 ${bam.baseName}_R2.fastq
"""
}
+
+process bam_to_bedgraph {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "${bam_id}"
+
+ input:
+ tuple val(bam_id), path(bam)
+
+ output:
+ tuple val(bam_id), path("*.bg"), emit: bedgraph
+
+ script:
+"""
+bedtools genomecov \
+ -ibam ${bam} \
+ -bg > ${bam.simpleName}.bg
+"""
+}
diff --git a/src/nf_modules/deeptools/main.nf b/src/nf_modules/deeptools/main.nf
index 4a60dabe..ccf3657a 100644
--- a/src/nf_modules/deeptools/main.nf
+++ b/src/nf_modules/deeptools/main.nf
@@ -1,4 +1,4 @@
-version = "3.0.2"
+version = "3.1.1"
container_url = "lbmc/deeptools:${version}"
process index_bam {
--
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