From 7b298e9246be8f85104f628cf9fe9024c5e1b6f9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 22 Jan 2021 15:21:43 +0100
Subject: [PATCH] nf_modules: add deeptools to DSL2

---
 src/nf_modules/deeptools/main.nf | 89 ++++++++++++++++++++++++++++++++
 src/nf_modules/sambamba/main.nf  |  2 +-
 2 files changed, 90 insertions(+), 1 deletion(-)
 create mode 100644 src/nf_modules/deeptools/main.nf

diff --git a/src/nf_modules/deeptools/main.nf b/src/nf_modules/deeptools/main.nf
new file mode 100644
index 00000000..ba2be7c5
--- /dev/null
+++ b/src/nf_modules/deeptools/main.nf
@@ -0,0 +1,89 @@
+version = "3.0.2"
+container_url = "lbmc/deeptools:${version}"
+
+process index_bam {
+  container = "${container_url}"
+  label "big_mem__cpus"
+  tag "$file_id"
+
+  input:
+    tuple val(file_id), path(bam)
+
+  output:
+    tuple val(file_id), path("*.bam*"), emit: bam
+
+  script:
+"""
+sambamba index -t ${task.cpus} ${bam}
+"""
+}
+
+process bam_to_bigwig {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+
+  publishDir "results/mapping/bigwig/", mode: 'copy'
+
+  input:
+    tuple val(file_id), path(bam), path(idx)
+
+  output:
+    tuple val(file_id), path("*.bw"), emit: bw
+
+  script:
+"""
+bamCoverage -p ${task.cpus} --ignoreDuplicates -b ${bam} -o ${file_id}.bw
+"""
+}
+
+process compute_matrix {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "${bed_file_id}"
+  publishDir "results/metagene/region_matrix/", mode: 'copy'
+
+  input:
+    tuple val(file_id), path(bw)
+    tuple val(bed_file_id), path(bed)
+
+  output:
+    tuple val(bed_file_id), path("*.mat.gz"), emit: matrix
+
+  script:
+"""
+computeMatrix scale-regions -S ${bw} \
+  -p ${task.cpus} \
+  -R ${bed} \
+  --beforeRegionStartLength 100 \
+  --afterRegionStartLength 100 \
+  -o ${bed_file_id}.mat.gz
+"""
+}
+
+process plot_profile {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  publishDir "results/metagene/region_matrix/", mode: 'copy'
+
+  input:
+    tuple val(file_id), path(matrix)
+
+  output:
+    tuple val(file_id), path("*.pdf"), emit: pdf
+
+  script:
+/*
+see more option at
+https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html
+*/
+"""
+plotProfile -m ${matrix} \
+  --plotFileFormat=pdf \
+  -out ${file_id}.pdf \
+  --plotType=fill \
+  --perGroup \
+  --plotTitle "${params.title}"
+"""
+}
diff --git a/src/nf_modules/sambamba/main.nf b/src/nf_modules/sambamba/main.nf
index 22614426..eb9bbb46 100644
--- a/src/nf_modules/sambamba/main.nf
+++ b/src/nf_modules/sambamba/main.nf
@@ -3,7 +3,7 @@ container_url = "lbmc/sambamba:${version}"
 
 process index_bam {
   container = "${container_url}"
-  label "big_mem__cpus"
+  label "big_mem_multi_cpus"
   tag "$file_id"
 
   input:
-- 
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