Cedars-Sinai Medical Center HPC

  • You will need HPC access from EIS, which can be requested in the Service Center.
  • You will need to load the nextflow module on the HPC before running any pipelines (module load nextflow). This should automatically load Java as well.
  • Run this with -profile cedars
  • By default this config file does not specify a queue for submission, and things will thus go to all.q. Because of that, the memory and cpu limits have been set accordingly.
  • We highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the $NXF_SINGULARITY_CACHE_DIR bash environment variable in your .bash_profile or .bashrc

Config file

See config file on GitHub

conf/cedars
//Profile config names for nf-core/configs
params {
    config_profile_description = 'Cedars-Sinai Medical Center HPC Profile'
    config_profile_contact     = 'Alex Rajewski (@rajewski)'
    config_profile_url         = 'https://www.cedars-sinai.edu/research/cores/informatics-computing/resources.html'
    max_memory                 = 90.GB
    max_cpus                   = 10
    max_time                   = 240.h
}


// Specify the queing system
executor {
    name = "sge"
}


process {
    resourceLimits = [
        memory: 90.GB,
        cpus: 10,
        time: 240.h
    ]
    penv         = 'smp'
    beforeScript = """
    module load 'singularity/3.6.0'
    """
}


singularity {
    enabled = true
}