nextflow.config

params {
    /* Input and output options */
    reads = "data/*{1,2}.fastq.gz"     // input reads (FASTA/FASTQ, gzip and bzip2 compressed files also supported)
    outdir = "./results"               // output directory
    single_end = false                 // true if the input reads are single-end
    interleaved = false                // true if the input paired-end reads are interleaved 
    kraken2_db = "kraken_db"           // Kraken2 database directory

    /* Kraken2 options */
    report_zero_counts = false         // reports taxa with no reads assigned to (or under) them
    
    /* Bracken options */
    read_len = 100                     // read length in bp

    /* Limits */
    max_cpus = 8
    max_memory = 64.GB
    max_time = 96.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 = 'Kraken2/Bracken workflow'
    mainScript = 'main.nf'
    version = '1.2.0'
}


/* 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
        }         
    }    
}