nf-core/configs: Alliance Canada Configuration

Configuration for running nextflow on the clusters of the Digital Research Alliance of Canada. Invoke by specifying -profile alliance_canada.

You also need to supply the name of the group under which you are working or whose resource allocation you want to use by running export SLURM_ACCOUNT=<def-user> before you run any nf-core pipeline. If you run nf-core frequently and always use the same resource allocation, you may find it more convenient to add the SLURM_ACCOUNT environment variable to your ~/.bashrc file.

For detailed information on running nf-core pipelines on Alliance clusters, please visit the documentation: https://docs.alliancecan.ca/wiki/Nextflow

If you run into issues, please contact Alliance Support: https://docs.alliancecan.ca/wiki/Technical_support

Config file

See config file on GitHub

conf/alliance_canada
params {
    config_profile_description  = 'Alliance Canada HPC config'
    config_profile_contact      = 'Jerry Li (@jerryakii)'
    config_profile_url          = 'https://docs.alliancecan.ca/wiki/Nextflow'
 
    max_time                    = 168.h
    max_cpus                    = 40
    max_memory                  = 186.GB
}
 
cleanup = true
 
singularity {
    enabled     = true
    autoMounts  = true
}
 
apptainer {
    autoMounts = true
}
 
// Group name for resource allocation must be supplied as environment variable
process {
    executor        = 'slurm'
    clusterOptions  = "--account=${System.getenv('SLURM_ACCOUNT')}"
    maxRetries      = 1
    errorStrategy   = { task.exitStatus in [125,139] ? 'retry' : 'finish' }
    cpu             = 1
    time            = '3h'
    resourceLimits = [
            memory: 186.GB,
            cpus: 40,
            time: 168.h
        ]
}
 
executor {
    pollInterval    = '60 sec'
    submitRateLimit = '60/1min'
    queueSize       = 100
}
 
// Cluster name is available as environment variable
// If not found, default to beluga as it has the lowest limits
hostname = "beluga"
try {
    hostname = "${System.getenv('HOSTNAME')}"
} catch (java.io.IOException e) {
    System.err.println("WARNING: Could not determine current cluster, defaulting to beluga")
}
 
// Cluster Beluga
if (hostname.startsWith("beluga")) {
    params.config_profile_description = 'Alliance Canada (Beluga) cluster profile provided by nf-core/configs.'
    params.max_memory = 186.GB
    params.max_cpus   = 40
    process {
        resourceLimits = [
            memory: 186.GB,
            cpus: 40,
            time: 168.h
        ]
    }
}
 
// Cluster Cedar
if (hostname.startsWith("cedar")) {
    params.config_profile_description = 'Alliance Canada (Cedar) cluster profile provided by nf-core/configs.'
    params.max_memory = 186.GB
    params.max_cpus   = 48
    params.max_time   = 672.h
    process {
        resourceLimits = [
            memory: 186.GB,
            cpus: 48,
            time: 672.h
        ]
    }
}
 
// Cluster Graham
if (hostname.startsWith("gra")) {
    params.config_profile_description = 'Alliance Canada (Graham) cluster profile provided by nf-core/configs.'
    params.max_memory = 186.GB
    params.max_cpus   = 40
    process {
        resourceLimits = [
            memory: 186.GB,
            cpus: 40,
            time: 168.h
        ]
    }
}
 
// Cluster Narval
if (hostname.startsWith("narval")) {
    params.config_profile_description = 'Alliance Canada (Narval) cluster profile provided by nf-core/configs.'
    params.max_memory = 249.GB
    params.max_cpus   = 64
    process {
        resourceLimits = [
            memory: 249.GB,
            cpus: 64,
            time: 168.h
        ]
    }
}
 
// Cluster Rorqual
if (hostname.startsWith("rorqual")) {
    params.config_profile_description = 'Alliance Canada (Rorqual) cluster profile provided by nf-core/configs.'
    params.max_memory = 512.GB
    params.max_cpus   = 64
    process {
        resourceLimits = [
            memory: 512.GB,
            cpus: 64,
            time: 168.h
        ]
    }
}