From a095fa9d642424a0d8e1f643bcb76c0d5696cb06 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 19 Dec 2018 16:11:40 +0100
Subject: [PATCH] deepTools: bam_to_bigwig working
---
src/nf_modules/deepTools/bam_to_bigwig.config | 13 +++++
src/nf_modules/deepTools/bam_to_bigwig.nf | 51 +++++++++++++++++++
2 files changed, 64 insertions(+)
create mode 100644 src/nf_modules/deepTools/bam_to_bigwig.nf
diff --git a/src/nf_modules/deepTools/bam_to_bigwig.config b/src/nf_modules/deepTools/bam_to_bigwig.config
index 6ecf0ac2..90eada5d 100644
--- a/src/nf_modules/deepTools/bam_to_bigwig.config
+++ b/src/nf_modules/deepTools/bam_to_bigwig.config
@@ -3,6 +3,9 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
+ withName: index_bam {
+ container = "sambamba:0.6.7"
+ }
withName: bam_to_bigwig {
container = "deeptools:3.0.2"
}
@@ -10,6 +13,16 @@ profiles {
}
psmn {
process{
+ withName: index_bam {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "sambamba/0.6.7"
+ 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'
+ }
withName: bam_to_bigwig {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "deepTools/3.0.2"
diff --git a/src/nf_modules/deepTools/bam_to_bigwig.nf b/src/nf_modules/deepTools/bam_to_bigwig.nf
new file mode 100644
index 00000000..012de76a
--- /dev/null
+++ b/src/nf_modules/deepTools/bam_to_bigwig.nf
@@ -0,0 +1,51 @@
+params.bam = "$baseDir/data/bam/*.bam"
+params.bamidx = "$baseDir/data/bam/*.idx"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+ .fromPath( params.bam )
+ .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+ .set { bam_files }
+
+bam_files.into{
+ bam_files_index;
+ bam_files_bigwig
+ }
+
+process index_bam {
+ tag "$file_id"
+ cpus 4
+
+ input:
+ set file_id, file(bam) from bam_files_index
+
+ output:
+ set file_id, "*.bam*" into indexed_bam_file
+
+ script:
+"""
+sambamba index -t ${task.cpus} ${bam}
+"""
+}
+
+bam_files_indexed = bam_files_bigwig.join(indexed_bam_file, by: 0)
+
+process bam_to_bigwig {
+ tag "$file_id"
+ cpus 4
+ publishDir "results/mapping/bigwig/", mode: 'copy'
+
+ input:
+ set file_id, file(bam), file(idx) from bam_files_indexed
+
+ output:
+ set file_id, "*.bw" into sorted_bam_files
+
+ script:
+"""
+bamCoverage -p ${task.cpus} --ignoreDuplicates -b ${bam} -o ${file_id}.bw
+"""
+}
+
--
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