From a12e9229cc323959eb49b1be866f3b9be5eb400b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 22 Jan 2021 14:32:46 +0100
Subject: [PATCH] nf_modules: masc2 add DSL2
---
src/nf_modules/macs2/main.nf | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
create mode 100644 src/nf_modules/macs2/main.nf
diff --git a/src/nf_modules/macs2/main.nf b/src/nf_modules/macs2/main.nf
new file mode 100644
index 00000000..9748cdc6
--- /dev/null
+++ b/src/nf_modules/macs2/main.nf
@@ -0,0 +1,35 @@
+version = "2.1.2"
+container_url = "lbmc/macs2:${version}"
+
+process peak_calling {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "${file_id}"
+ publishDir "results/peak_calling/${file_id}", mode: 'copy'
+
+ input:
+ tuple val(file_id), path(bam_ip), path(bam_control)
+
+ output:
+ path "*", emit: peak
+ path "*_report.txt", emit: report
+
+ script:
+/* remove --nomodel option for real dataset */
+"""
+macs2 callpeak \
+ --treatment ${file_ip} \
+ --call-summits "True"\
+ --control ${file_control} \
+ --keep-dup "auto" \
+ --name ${file_id} \
+ --gsize ${params.genome_size} 2> \
+ ${file_ip}_macs2_report.txt
+
+if grep -q "ERROR" ${file_ip}_macs2_report.txt; then
+ echo "MACS2 error"
+ exit 1
+fi
+"""
+}
+
--
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