nextflow.config

profiles {
    standard {
        process {
            executor  = 'local'
        }
    }
    // UBC ARC Sockeye
    sockeye {
        env.JULIA_PKG_USE_CLI_GIT = 'true'
    	apptainer.enabled = true
	process {
	    scratch        = true
	    executor       = 'pbspro'
            container      = 'docker://alexandrebouchardcote/default:0.1.4'
	    clusterOptions = 'YOUR_CLUSTER_OPTIONS'
	    module         = 'apptainer'
	    cpus           = 1
	    memory         = 4.GB
	    time           = '2h'
	}
    }
    // Compute Canada
    CC {
	env.JULIA_PKG_USE_CLI_GIT = 'true'
        apptainer.enabled = true
        apptainer.autoMounts = true
    	process {
	    scratch        = true
	    executor       = 'slurm'
            container      = 'docker://alexandrebouchardcote/default:0.1.4'
	    clusterOptions = 'YOUR_CLUSTER_OPTIONS'
	    module         = 'apptainer'
	    cpus           = 1
	    memory         = 4.GB
            time           = '2h'
	}
    }
}

executor {
    $local {
        cpus = 4
        //memory = 12.GB
    }
    $pbspro {
        submitRateLimit = '120/1min'
        queueSize = 500
    }
    $slurm {
        submitRateLimit = '120/1min'
        queueSize = 500
    }
}