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

cedars.config
//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 {
  penv = 'smp'
  beforeScript =
  """
  module load 'singularity/3.6.0'
  """
}
 
singularity {
  enabled = true
}