nextflow.config

params {
    /* Input and output options */
    genomes = "data/*.fa"             // input contigs or genomes in FASTA format
    outdir = "./results"              // output directory
    
    /* General options (except Anvi'o kofam) */
    metagenome = false                // Improve gene predictions for metagenomes and
                                      // short sequences (<100kbp, e.g viruses)
    
    /* Prokka options */
    skip_prokka = false               // skip prokka
    prokka_kingdom = "Bacteria"       // Archaea, Bacteria, Mitochondria, Viruses

    /* eggNOG options */
    run_eggnog = false                // run eggNOG (database required)
    eggnog_db = "none"                // eggNOG v5.0 db dir. 'none': download from Internet
    eggnog_db_mem = false             // store the eggNOG sqlite DB into memory (~44GB memory
                                      // required). This increase the annotation speed.

    /* KofamScan options */
    run_kofamscan = false             // run KofamScan (database required)
    kofamscan_db = "none"             // KofamScan db dir. 'none': download from Internet

    /* Anvi'o kofam options */
    run_anvio_kofam = false           // run KofamScan
    anvio_kofam_db = "none"           // Anvi'o Kofam db dir. 'none': download from Internet
    
    /* Limits */
    max_cpus = 6
    max_memory = 64.GB
    max_time = 480.h
}


/* Docker options */
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'


/* Import process configuration file*/
includeConfig 'process.config'


/* Manifest */
manifest {
    homePage = 'metashot.github.io'
    description = 'Annotation pipeline for prokaryotic genomes and metagenomes'
    mainScript = 'main.nf'
    version = '3.0.0'
}


/* Functions */
def check_max(obj, max) {
    // see https://github.com/nextflow-io/nextflow/issues/640
    if( obj instanceof nextflow.util.MemoryUnit ) {
        try {
            def max_type = max as nextflow.util.MemoryUnit
            return obj.compareTo(max_type) == 1 ? max_type : obj
        }   
        catch( all ) {
            println "ERROR: invalid max memory '${max}', using default value: $obj"
            return obj
        }   
    }
    if( obj instanceof nextflow.util.Duration ) {
        try {
            def max_type = max as nextflow.util.Duration
            return obj.compareTo(max_type) == 1 ? max_type : obj
        }   
        catch( all ) {
            println "ERROR: invalid max time '${max}', using default value $obj"
            return obj
        }         
    }
    if( obj instanceof Integer ) {
        try {
            return Math.min(obj, max as int)
        }   
        catch( all ) {
            println "ERROR: invalid max cpus '${max}', using default value $obj"
            return obj
        }         
    }    
}