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Laurent Modolo authoredLaurent Modolo authored
training_dataset.config 6.96 KiB
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
withName: build_synthetic_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: index_fasta {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: mapping_fastq_paired {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: bam_2_fastq_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: mapping_fastq_single {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: bam_2_fastq_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
}
}
singularity {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
withName: build_synthetic_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: index_fasta {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: mapping_fastq_single {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: mapping_fastq_paired {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: bam_2_fastq_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: bam_2_fastq_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
}
}
psmn {
process{
withName: build_synthetic_bed {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
withName: fasta_from_bed {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
withName: index_fasta {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
memory = "20GB"
time = "12h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
}
withName: mapping_fastq_paired {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/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'
}
withName: bam_2_fastq_paired {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
}
withName: sort_bam_paired {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/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'
penv = 'openmp16'
}
withName: index_bam_paired {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
}
withName: mapping_fastq_single {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/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'
}
withName: bam_2_fastq_single {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
}
withName: sort_bam_single {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/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'
penv = 'openmp16'
}
withName: index_bam_single {
beforeScript = "./src/conda_psmn.sh"
conda = "$CONDA_ENVS/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'
penv = 'openmp16'
}
}
}
}