params {
    reference = null

    // Config options
    config_profile_name = null
    config_profile_description = null
    custom_config_version = 'master'
    custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_contact = null
    config_profile_url = null

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory = '128.GB'
    max_cpus = 16
    max_time = '240.h'
}

process {
    errorStrategy = 'finish'
    time = '7d'

    withName: 'HAPLINK_ML_HAPLOTYPES' {
        ext.ml_args = """
        --simulated-reads \\
        --overlap-min 20 \\
        --overlap-max 8000 \\
        """
    }
}

try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

singularity.enabled = true

env {
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
}