process.config

process {

    errorStrategy = 'terminate'

    // Deinterleave
    withName: deinterleave {
        container = 'metashot/bbtools:38.79-2'
        cpus = check_max(2, params.max_cpus) // reformat will generally use over 2 CPU cores on average since the I/O is in separate threads
        memory = check_max(4.GB, params.max_memory)
        time = params.max_time
    }

    // Reads stats
    withName: raw_reads_stats {
        container = 'metashot/bbtools:38.79-2'
        cpus = check_max(4, params.max_cpus)
        memory = check_max(4.GB, params.max_memory)
        time = params.max_time
    }

    // Kraken2
    withName: kraken2 {
        container = 'metashot/kraken2:2.1.2-1'
        cpus = check_max(4, params.max_cpus)
        memory = params.max_memory
        time = params.max_time
    }

    // Bracken
    withName: bracken {
        container = 'metashot/kraken2:2.1.2-1'
        cpus = 2
        memory = check_max(8.GB, params.max_memory)
        time = params.max_time
    }

    // Utils
    withName: 'combine_kraken2_reports|combine_kraken2_mpa|combine_bracken|combine_bracken_reports|combine_bracken_mpa' {
        container = 'metashot/kraken2:2.1.2-1'
        cpus = 2
        memory = check_max(8.GB, params.max_memory)
        time = params.max_time
        errorStrategy = 'ignore'
    }
}