From 0d885dcd6b9a46cbbfdc7d628502e7b16bbc0fe8 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 18 Feb 2021 09:48:57 +0100
Subject: [PATCH] macs3: add main.nf
---
src/nf_modules/macs3/main.nf | 69 ++++++++++++++++++++++++++++++++++++
1 file changed, 69 insertions(+)
create mode 100644 src/nf_modules/macs3/main.nf
diff --git a/src/nf_modules/macs3/main.nf b/src/nf_modules/macs3/main.nf
new file mode 100644
index 00000000..b5b14056
--- /dev/null
+++ b/src/nf_modules/macs3/main.nf
@@ -0,0 +1,69 @@
+version = "3.0.0a6"
+container_url = "lbmc/macs3:${version}"
+
+process peak_calling {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "${file_id}"
+
+ 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 ${bam_ip.simpleName} \
+ --gsize ${macs3_genome_size} 2> \
+ ${bam_ip.simpleName}_macs3_report.txt
+
+if grep -q "ERROR" ${bam_ip.simpleName}_macs3_report.txt; then
+ echo "MACS3 error"
+ exit 1
+fi
+"""
+}
+
+process peak_calling_bg {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "${file_id}"
+
+ input:
+ tuple val(file_id), path(bg_ip), path(bg_control)
+
+ output:
+ path "*", emit: peak
+ path "*_report.txt", emit: report
+
+ script:
+/* remove --nomodel option for real dataset */
+"""
+awk '{print $1"\t"$2"\t"$3"\t.\t+\t"$4}' ${file_ip} > \
+ ${file_ip.simpleName}.bed
+awk '{print $1"\t"$2"\t"$3"\t.\t+\t"$4}' ${file_control} > \
+ ${file_control.simpleName}.bed
+macs2 callpeak \
+ --treatment ${file_ip.simpleName}.bed \
+ --call-summits "True"\
+ --control ${file_control.simpleName}.bed \
+ --keep-dup "auto" \
+ --name ${bam_ip.simpleName} \
+ --gsize ${macs3_genome_size} 2> \
+ ${bam_ip.simpleName}_macs3_report.txt
+
+if grep -q "ERROR" ${bam_ip.simpleName}_macs3_report.txt; then
+ echo "MACS3 error"
+ exit 1
+fi
+"""
+}
+
--
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