nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NorwegianVeterinaryInstitute/DPI Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// Global default params, used in configs

params {
    // Input
    input			= null
    
    // Bakta Annotation options
    baktaDB         = null
    training        = null 
    genus           = null
    species         = null

    // Database
    // Column with comments: If there are spaces within your comment you must have the comment ' '  and the  "" around, otherwise it wont work
    comment         = "'NA'" 
    // Database name: sqlite database - needs .sqlite extension
    sqlitedb        = "out.sqlite"

    // general options 
	time_multiplier		= 1
    publish_dir_mode    = "copy"
    debug               = false
    
    }

// Profiles 
includeConfig 'conf/profiles.config' 

conda { createTimeout = "120 min" }

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

// Test config are in profiles


// Manifest
manifest {
    name            = 'NorwegianVeterinaryInstitute/DPI'
    author          = 'Eve Fiskebeck, Håkon Kaspersen'
    homePage        = 'https://github.com/NorwegianVeterinaryInstitute/DPI'
    description     = 'DPI: a Tool that reports Differences between Pairs of Isolates'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=23.04.4'
    version         = '0.2'
    }


// Define variables to prevent local R libraries from conflicting with the container
env {
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
}

// 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
        }
    }
}