nextflow.config

manifest {
    mainScript = 'main.nf'
    nextflowVersion = '>=20.01.0'
}

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

    // folder structure
    output = 'results'

    // input 
    genomes = ''
    proteins = ''
    list = false
    // for one-vs-all switch
    genome = false
    protein = false

    // Prokka
    gcode = 0

    // DIAMOND or BLASTP protein alignment
    blastp = false
    evalue = '1e-5'
    seqidentity = 0.4
    alnlength = 0.5

    // Plot POCP heatmap
    width = 16
    height = 8

    // location for storing the conda environments
    condaCacheDir = 'conda'
    singularityCacheDir = 'singularity'
}


profiles {
    
    ////////////////////////////////////////////////////
    // executors

    local {
        executor {
            name = "local"
            cpus = params.max_cores
            memory = params.memory
        }
        includeConfig 'configs/local.config'
    }

    slurm {
        executor {
            name = "slurm"
            queueSize = 100
            // exitReadTimeout = "360 sec"
            // submitRateLimit = '1 / 2 s'
            // pollInterval = '30 sec'
        }
        process.cache = "lenient"
        includeConfig 'configs/nodes.config'
    }


    ////////////////////////////////////////////////////
    // engines 

    conda {
        conda{
            enabled = true
            cacheDir = params.condaCacheDir
            timeout = '45 min'
        }
        includeConfig 'configs/conda.config'
    }
    mamba {
        conda{
            enabled = true
            cacheDir = params.condaCacheDir
            timeout = '45 min'
            useMamba = true
        }
        includeConfig 'configs/conda.config'
    }
    docker {
        docker { 
            enabled = true
        }
        includeConfig 'configs/container.config'
    }

    singularity {
        singularity { 
                enabled = true
                autoMounts = true
                cacheDir = params.singularityCacheDir
        }
        includeConfig 'configs/container.config'
    }    

    ////////////////////////////////////////////////////
    // pre-configured 
    // local execution with conda
    standard {
        executor {
            name = "local"
            cpus = params.max_cores
            memory = params.memory
        }
        conda { 
            cacheDir = params.condaCacheDir 
            enabled = true
        }
        includeConfig 'configs/local.config'
        includeConfig 'configs/conda.config' 
    }

}