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: bioHPC compute nodes are submit hosts. This means you can submit the nextflow head job via sbatch.
NB: Sometimes you may want to have jobs submitted ‘locally’ in a large nextflow job. Details on this can be found here https://doku.lrz.de/nextflow-on-hpc-systems-test-operation-788693597.html
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'
array = 25
}
executor {
$slurm {
queueStatInterval = '10 min'
pollInterval = '30 sec'
submitRateLimit = '25sec'
}
}
charliecloud {
enabled = true
writeFake = false
}
params {
params.max_time = 14.d
params.max_cpus = 80
params.max_memory = 3.TB
}
executor
contact
