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_DIRbash environment variable in your.bash_profileor.bashrc
Config file
//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
}
executor
sge
contact
