From b25a6418a9362ce94d8412b1b1fa7c7caa8dc4c7 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 19 Dec 2018 16:27:14 +0100
Subject: [PATCH] deepTools: add compute_matrix module
---
src/nf_modules/deepTools/bam_to_bigwig.config | 7 ++--
src/nf_modules/deepTools/bam_to_bigwig.nf | 1 -
.../deepTools/compute_matrix.config | 25 +++++++++++
src/nf_modules/deepTools/compute_matrix.nf | 41 +++++++++++++++++++
src/nf_modules/deepTools/tests.sh | 2 +-
5 files changed, 71 insertions(+), 5 deletions(-)
create mode 100644 src/nf_modules/deepTools/compute_matrix.config
create mode 100644 src/nf_modules/deepTools/compute_matrix.nf
diff --git a/src/nf_modules/deepTools/bam_to_bigwig.config b/src/nf_modules/deepTools/bam_to_bigwig.config
index 90eada5d..c1b71cb0 100644
--- a/src/nf_modules/deepTools/bam_to_bigwig.config
+++ b/src/nf_modules/deepTools/bam_to_bigwig.config
@@ -28,9 +28,10 @@ profiles {
module = "deepTools/3.0.2"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- memory = "20GB"
- time = "12h"
- queue = 'monointeldeb128'
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
}
}
}
diff --git a/src/nf_modules/deepTools/bam_to_bigwig.nf b/src/nf_modules/deepTools/bam_to_bigwig.nf
index 012de76a..3507337d 100644
--- a/src/nf_modules/deepTools/bam_to_bigwig.nf
+++ b/src/nf_modules/deepTools/bam_to_bigwig.nf
@@ -1,5 +1,4 @@
params.bam = "$baseDir/data/bam/*.bam"
-params.bamidx = "$baseDir/data/bam/*.idx"
log.info "bams files : ${params.bam}"
diff --git a/src/nf_modules/deepTools/compute_matrix.config b/src/nf_modules/deepTools/compute_matrix.config
new file mode 100644
index 00000000..cb32bf55
--- /dev/null
+++ b/src/nf_modules/deepTools/compute_matrix.config
@@ -0,0 +1,25 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: compute_matrix {
+ container = "deeptools:3.0.2"
+ }
+ }
+ }
+ psmn {
+ process{
+ withName: bam_to_bigwig {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "deepTools/3.0.2"
+ executor = "sge"
+ clusterOptions = "-m e -cwd -V"
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/deepTools/compute_matrix.nf b/src/nf_modules/deepTools/compute_matrix.nf
new file mode 100644
index 00000000..53b4b195
--- /dev/null
+++ b/src/nf_modules/deepTools/compute_matrix.nf
@@ -0,0 +1,41 @@
+params.bam = "$baseDir/data/bigwig/*.bw"
+params.bed = "$baseDir/data/annot/*.bed"
+
+log.info "bigwig files : ${params.bw}"
+log.info "bed files : ${params.bed}"
+
+Channel
+ .fromPath( params.bw )
+ .ifEmpty { error "Cannot find any bigwig files matching: ${params.bw}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+ .set { bw_files }
+
+Channel
+ .fromPath( params.bed )
+ .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+ .set { bed_files }
+
+process compute_matrix {
+ tag "$file_id"
+ cpus 4
+ echo true
+ publishDir "results/mapping/region_matrix/", mode: 'copy'
+
+ input:
+ set bw_file_id, file(bw) from bw_files.collect()
+ set bed_file_id, file(bed) from bed_files.collect()
+
+ output:
+ set bed_file_id, "*.mat.gz" into region_matrix
+
+ script:
+"""
+computeMatrix scale-regions -S ${bw} \
+ -p ${task.cpus} \
+ -R ${bed} \
+ --beforeRegionStartLength 100 \
+ --afterRegionStartLength 100 \
+ -o ${bed_file_id}.mat.gz
+"""
+}
diff --git a/src/nf_modules/deepTools/tests.sh b/src/nf_modules/deepTools/tests.sh
index 46816151..63b8434e 100755
--- a/src/nf_modules/deepTools/tests.sh
+++ b/src/nf_modules/deepTools/tests.sh
@@ -2,5 +2,5 @@
./nextflow src/nf_modules/deepTools/bam_to_bigwig.nf -c src/nf_modules/deepTools/bam_to_bigwig.config -profile docker --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
-./nextflow src/nf_modules/deepTools/compute_matrix.nf -c src/nf_modules/deepTools/compute_matrix.config -profile docker --bam "results/mapping/bigwig/*.bw"
+./nextflow src/nf_modules/deepTools/compute_matrix.nf -c src/nf_modules/deepTools/compute_matrix.config -profile docker --bw "results/mapping/bigwig/*.bw" --bed "data/tiny_dataset/annot/tiny.bed"
--
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