nf-core/configs: 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

See config file on GitHub

conf/jax
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
}