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profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$build_synthetic_bed {
container = "bedtools:2.25.0"
}
$fasta_from_bed {
container = "bedtools:2.25.0"
}
$index_fasta {
container = "bowtie2:2.3.4.1"
}
$mapping_fastq_paired {
container = "bowtie2:2.3.4.1"
}
$bam_2_fastq_paired {
container = "samtools:1.7"
}
$mapping_fastq_single {
container = "bowtie2:2.3.4.1"
}
$bam_2_fastq_single {
container = "samtools:1.7"
}
}
}
sge {
process{
$build_synthetic_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$fasta_from_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$index_fasta {
beforeScript = "module purge; module load Bowtie2/2.3.4.1"
}
$mapping_fastq_paired {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
$bam_2_fastq_paired {
beforeScript = "module purge; module load SAMtools/1.7"
}
$mapping_fastq_single {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
$bam_2_fastq_single {
beforeScript = "module purge; module load SAMtools/1.7"
}
}
}
}