nf-core/configs: biohpc_gen
BioHPC Genomics (biohpc_gen) cluster profile provided by nf-core/configs
BioHPC Genomics (BIOHPC_GEN) Configuration
All nf-core pipelines have been successfully configured for use on the BioHPC Genomics (biohpc_gen) cluster that is housed at the Leibniz Rechenzentrum (LRZ) for research groups at the Faculty of Biology of the Ludwig-Maximilians-University (LMU) in Munich.
To use, run the pipeline with -profile biohpc_gen. This will download and launch the biohpc_gen.config which has been pre-configured with a setup suitable for the biohpc_gen cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Charliecloud container before execution of the pipeline.
NB: You will need an account to use the LRZ Linux cluster as well as group access to the biohpc_gen cluster in order to run nf-core pipelines.
To correctly submit jobs into the biohpc_gen cluster the SLURM_CLUSTERS variable needs to be set:
export SLURM_CLUSTERS=biohpc_gen
Recent versions can be installed via spack and made available as a module.
Cluster specific instructions to load spack:
module load spack
module load user_spack
We recommend to use charliecloud >= 0.35.
spack install charliecloud@0.35
spack module tcl refresh charliecloud
module avail charliecloud
In addition we recommend using nextflow >= 24.04.2. This can be installed via spack:
spack install nextflow@24.04.2
spack module tcl refresh nextflow
module avail nextflow
These are then available as modules (please confirm the module name using module avail)
## Load Nextflow and Charliecloud environment modules
module load nextflow/24.04.2-gcc12 charliecloud/0.35-gcc12
NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes.
Config file
//Profile config names for nf-core/configs
params {
config_profile_description = 'BioHPC Genomics (biohpc_gen) cluster profile provided by nf-core/configs'
config_profile_contact = 'Niklas Schandry (@nschan)'
config_profile_url = 'https://collab.dvb.bayern/display/LMUBioHPCGenomics/BioHPC+Genomics'
}
process {
resourceLimits = [
memory: 3.TB,
cpus: 80,
time: 14.d
]
executor = 'slurm'
queue = { task.memory <= 1536.GB ? (task.time > 2.d || task.memory > 384.GB ? 'biohpc_gen_production' : 'biohpc_gen_normal') : 'biohpc_gen_highmem' }
clusterOptions = '--clusters=biohpc_gen'
}
charliecloud {
enabled = true
writeFake = false
}
params {
params.max_time = 14.d
params.max_cpus = 80
params.max_memory = 3.TB
}
executor
contact
