medair.config

//Profile config names for nf-core/configs
params {
    config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)'
    config_profile_contact     = 'Clinical Genomics, Gothenburg (cgg-rd@gu.se, cgg-it@gu.se)'
    config_profile_url         = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/'
}

//Nextflow parameters
singularity {
    enabled  = true
    cacheDir = "/apps/bio/dependencies/nf-core/singularities"
}

profiles {

    wgs {
        process {
            resourceLimits         = [
                memory: 128.GB,
                cpus: 40,
                time: 48.h
            ]
            queue                  = 'wgs.q'
            executor               = 'sge'
            penv                   = 'mpi'
            process.clusterOptions = '-l excl=1'
            params.max_cpus        = 40
            params.max_time        = 48.h
            params.max_memory      = 128.GB
        }
    }

    production {
        process {
            resourceLimits         = [
                memory: 128.GB,
                cpus: 40,
                time: 480.h
            ]
            queue                  = 'production.q'
            executor               = 'sge'
            penv                   = 'mpi'
            process.clusterOptions = '-l excl=1'
            params.max_cpus        = 40
            params.max_time        = 480.h
            params.max_memory      = 128.GB
        }
    }
}

//Specific parameter for pipelines that can use Sentieon (e.g. nf-core/sarek, nf-core/raredisease)
process {
    withLabel: sentieon {
        container = "/apps/bio/singularities/sentieon-211204-peta.simg"
    }
}