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profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
withName: mapping_fastq {
cpus = 4
}
}
}
singularity {
singularity.enabled = true
process {
withName: mapping_fastq {
cpus = 4
container = "file://bin/hisat2:2.1.0.img"
}
}
}
sge {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
cpus = 16
time = "12h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
}
}
}
ccin2p3 {
process{
withName: mapping_fastq {
beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/usr/bin:$PATH"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
memory = "10GB"
time = "24h"
}
}
}