prok-classify/nextflow.config at master · metashot/prok-classify · GitHub

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params {
    /* Input and output options */
    genomes = "data/*.fa"          // input genomes (FASTA format)
    gtdbtk_db = "gtdbtk_db"        // GTDB database
    outdir = "./results"           // output directory

    /* Limits */
    max_cpus = 8
    max_memory = 70.GB
    max_time = 168.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 = 'Assign objective taxonomic classifications to bacterial and archaeal genomes'
    mainScript = 'main.nf'
    version = '1.3.0'
}


/* 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
        }
    }
}