JAX Configuration
All nf-core pipelines have been successfully configured for use on the JAX Sumner cluster at The Jackson Laboratory.
To use, run the pipeline with -profile jax. This will download and launch the jax.config which has been pre-configured with a setup suitable for JAX Sumner cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline and slurm will be used as well.
NB: You will need an account to use the HPC cluster JAX in order to run the pipeline. If in doubt contact IT. NB: Nextflow should not be executed on the login nodes. If in doubt contact IT.
Config file
params {
config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.'
config_profile_contact = 'Bill Flynn (@flynnb)'
config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx'
singularity_cache_dir = '/flashscratch/singularity_cache_nfcore'
}
executor.$slurm.queueSize = 250
process {
resourceLimits = [
memory: 320.GB,
cpus: 32,
time: 336.h
]
executor = "slurm"
queue = "compute"
clusterOptions = { task.time < 72.h ? '-q batch' : '-q long' }
module = "slurm"
beforeScript = 'module load singularity'
}
singularity {
enabled = true
autoMounts = true
cacheDir = params.singularity_cache_dir
}
params {
max_memory = 320.GB
max_cpus = 32
max_time = 336.h
}
executor
slurm
contact
