nextflow.config

params {
    ref_fasta             = null
    bai                   = null 
    ref_fasta_fai         = null
    accesibility          = null
    accesibility_bed      = null
    publish_dir_mode      = 'link'
    // Config options
    custom_config_version = 'master'
    custom_config_base    = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"

}

// Load base config
includeConfig 'conf/base.config'

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'

// Load nf-core custom profiles from different Institutions
    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")
    }

profiles {
    test { includeConfig 'conf/test.config' }
    real_data { includeConfig 'conf/real_data.config' }
}


// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}