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fastqdump.nf
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indexing.config 1.66 KiB
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
withName: index_fasta {
container = "bowtie2:2.3.4.1"
cpus = 4
}
}
}
singularity {
singularity.enabled = true
process {
withName: index_fasta {
container = "file://bin/bowtie2:2.3.4.1.img"
cpus = 4
}
}
}
psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "bowtie2/2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
memory = "20GB"
time = "12h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
}
}
}
ccin2p3_conda {
process{
withName: index_fasta {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
queue = 'huge'
}
}
}
ccin2p3 {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
}
}
}