Unverified Commit d89578cf authored by Laurent Modolo's avatar Laurent Modolo
Browse files

mapping.nf: fix cpus number

parent 66fc2216
......@@ -3,7 +3,7 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
withname: mapping_fastq {
withname: index_fasta {
container = "bowtie2:2.3.4.1"
}
withname: mapping_fastq {
......@@ -19,23 +19,19 @@ profiles {
}
psmn {
process{
withname: mapping_fastq {
withname: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
}
withname: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
......@@ -46,7 +42,6 @@ profiles {
module = "sambamba/0.6.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
......@@ -57,7 +52,6 @@ profiles {
module = "sambamba/0.6.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
......
params.fasta = "$baseDir/data/bam/*.fasta"
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
params.contig = ""
params.cpus = 10
log.info "fasta files : ${params.fasta}"
log.info "fastq files : ${params.fastq}"
......@@ -37,7 +38,6 @@ cp ${fasta} contigs.fasta
process index_fasta {
tag "$fasta.baseName"
cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
......@@ -59,7 +59,7 @@ fi
process mapping_fastq {
tag "$pair_id"
cpus 4
cpus params.cpus
input:
set pair_id, file(reads) from fastq_files
......@@ -90,7 +90,8 @@ fi
process sort_bam {
tag "$file_id"
cpus 4
cpus params.cpus
publishDir "results/mapping/bams/", mode: 'copy'
input:
......@@ -107,7 +108,7 @@ sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
process index_bam {
tag "$file_id"
cpus 4
cpus params.cpus
publishDir "results/mapping/bams/", mode: 'copy'
input:
......
......@@ -3,7 +3,7 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
withname: mapping_fastq {
withname: index_fasta {
container = "bowtie2:2.3.4.1"
}
}
......@@ -13,13 +13,11 @@ profiles {
withname: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
}
}
}
......
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