nextflow.config

// config to run pATLAS_mash_screen.nf script
manifest {
    author = "Tiago F. Jesus"
    description = "This Nextflow pipeline is an implementation of mash-wrapper.py " +
        "and PlasmidUNCover.py. It will output a JSON file that can be " +
        "imported into pATLAS."
}

// sets PYTHONPATH for utils to be available for templates
env {
    PYTHONPATH = "$baseDir/templates:$baseDir/templates/assemblerflow_utils:\$PYTHONPATH"
}

//manifest.mainScript = 'main.nf'

// default values for params
params {
    kMer = 21 //this is never used xD
    pValue = 0.05
    identity = 0.9
    mash_distance = 0.1
    shared_hashes = 0.8
    noWinner = false
    //bowtie2 unique options
    trim5 = 0
    cov_cutoff = 0.60    // cutoff for the coverage in mapping approach

    reads = 'reads/*_{1,2}.fastq*' //this accepts that fastq.gz files are in reads folder
    fasta = 'fasta/*.fas' //home/data

    mash_screen = false  //boolean to run mash screen. By default it is true
    mapping = false     //boolean to check if mapping approach is enabled. By default it is false
    assembly = false    //boolean to run assembly based mash dist. By default it is set to false
    singleEnd = false
    help = false
    version = "1.1.0"
}

process {
    $mashScreen.container = 'tiagofilipe12/patlasflow_mash_screen:1.6.0'
    $mashOutputJson.container = 'tiagofilipe12/patlasflow_mash_screen:1.6.0'
    $runMashDist.container = 'tiagofilipe12/patlasflow_mash_screen:1.6.0'
    $mashDistOutputJson.container = 'tiagofilipe12/patlasflow_mash_screen:1.6.0'
    $mappingBowtie.container = 'tiagofilipe12/patlasflow_mapping:1.6.0'
    $mappingBowtie.scratch = true
    $samtoolsView.container = 'tiagofilipe12/patlasflow_mapping:1.6.0'
    $samtoolsView.scratch = true
    $jsonDumpingMapping.container = 'tiagofilipe12/patlasflow_mapping:1.6.0'
}

// this should be passed with the -profile mash_screen
profiles {
    // standard uses executor local and docker
    standard {
        docker.enabled = true
    }
    singularity {
        cacheDir = "$HOME/.singularity_cache"
        singularity.enabled = true
    }
    slurm {
        process.executor  = "slurm"
        process.errorStrategy = "retry"
        // option exclusive for imm-lobo cluster
        //process.clusterOptions = "--exclude=compute-1"
        process.maxRetries = 3
        shifter.enabled = true
        process {
            $mashScreen.cpus = 4
            $mashOutputJson.cpus = 1
            $runMashDist.cpus = 4
            $mashDistOutputJson.cpus = 1
            $mappingBowtie.cpus = 10
            $samtoolsView.cpus = 10
            $jsonDumpingMapping.cpus = 1
            $fullConsensus.cpus = 1

            $mashScreen.memory = { 4.GB * task.attempt }

            $mashOutputJson.memory = "1GB"

            $runMashDist.memory = { 4.GB * task.attempt }

            $mashDistOutputJson.memory = "1GB"

            $mappingBowtie.memory = { 10.GB * task.attempt }
            //$mappingBowtie.scratch = true

            $samtoolsView.memory = { 10.GB * task.attempt }
            //$samtoolsView.scratch = true

            $jsonDumpingMapping.memory = "1GB"

            $fullConsensus.memory = "1GB"
        }
    }
}