nextflow.config

manifest {
    mainScript = 'main.nf'
    nextflowVersion = '>=22.04.0'
}

// default parameters
params {
    max_cores = Runtime.runtime.availableProcessors()
    cores = Runtime.runtime.availableProcessors().intdiv(4)
    memory = 8.GB
    max_memory = 24.GB
    help = false
    profile = false

    // input
    nano = ''
    illumina = ''
    sra = ''
    list = false

    bbduk = ''
    index_ont = ''
    index_fna = ''
    index_ill = ''

    host = ''
    species = ''
    phix = true
    dcs = true

    // parameters
    gsize = ''
    length = '500'
    model = 'r941_min_sup_g507'
    // SRA key
    key = ""

    // databases
    dia_db = false

    // workflow adjustments
    assemblerHybrid = 'spades'
    assemblerLong = 'flye'

    // folder structure
    output = 'results'

    // ENA-specific params
    study = ''
    sample = ''
    run = ''

    // optional profile configurations, only necessary for HPC LSF execution
    cloudDatabase = 'nextflow-databases'
    singularityCacheDir = 'singularity'
    condaCacheDir = 'conda'
}

profiles {

    // executors
    local {
        executor {
            name = "local"
            cpus = params.max_cores
            memory = params.max_memory
        }
        params.cloudProcess = false
        params.cloudDatabase = false
        includeConfig 'configs/local.config'
    }

    lsf {
        executor {
            name = "lsf"
            queueSize = 200
        }        
        params.cloudProcess = true
        process.cache = "lenient"
        includeConfig 'configs/node.config'
    }

    slurm {
        executor {
            name = "slurm"
            queueSize = 200
        }        
        params.cloudProcess = true
        process.cache = "lenient"
        includeConfig 'configs/node.config'
    }

    // engines
    docker { 
        docker { enabled = true }
        includeConfig 'configs/container.config'
    }

    singularity {
        singularity { 
                enabled = true
                autoMounts = true
                cacheDir = params.singularityCacheDir
                envWhitelist = "HTTPS_PROXY,HTTP_PROXY,http_proxy,https_proxy,FTP_PROXY,ftp_proxy"
        }
        includeConfig 'configs/container.config'
    }

    mamba { 
        conda {
            enabled = true
            cacheDir = params.condaCacheDir
            useMamba = true
        }
        includeConfig 'configs/conda.config'
    }

    conda { 
        conda {
            enabled = true
            cacheDir = params.condaCacheDir
        }
        includeConfig 'configs/conda.config'
    }

    // pre-merged
    ebi {
        params.cloudProcess = true
  	    params.cloudDatabase = "/hps/nobackup2/production/metagenomics/$USER/nextflow-databases/"
  	    params.cachedir = "/hps/nobackup2/singularity/$USER"
        includeConfig 'configs/lsf.config' }

    yoda {
        params.cloudProcess = true
  	    params.cloudDatabase = "/hps/nobackup2/metagenomics/$USER/nextflow-databases/"
  	    params.cachedir = "/hps/nobackup2/metagenomics/$USER/singularity"
        includeConfig 'configs/lsf.config' }
}