nextflow.config

manifest {
    /* Homepage of project */
    homePage = 'https://github.com/m-bull/nextflow-flu'

    /* Description of project */
    description = 'A flu analysis pipeline leaning heavily on Auir: https://github.com/cdeanj/auir'

    /* Main pipeline script */
    mainScript = 'flu.nf'

    /* Default repository branch */
    defaultBranch = 'master'
}


docker {
    /* Enables Docker execution */
    enabled = true

    /* Fixes ownership of outputs created inside of a Docker container */
    fixOwnership = true
}

params {
    /* Location of forward and reverse read pairs */
    reads = ""

    /* Location of reference genome index files */
    index = ""

    /* Location of reference genome */
    host = ""

    /* Location of adapter sequences */
    adapters = "data/adapters/nextera.fa"

    /* Location of tab delimited adapter sequences */
    fqc_adapters = "data/adapters/nextera.tab"

    /* Output directory */
    output = "./test"

    /* Number of threads */
    threads = 5

    /* Display help message */
    help = false
}

process {
    $AlignReadsToHost {
        container = "mbull/bioinformatics-containers:bwa"
        maxForks = 4
    }
    $RunBlast {
        container = "cdeanj/auir:makeblastdb"
        maxForks = 4
    }
    $RunIVA {
        container = "mbull/bioinformatics-containers:iva"
        maxForks = 4
    }
    $BAMToFASTQ {
        container = "cdeanj/auir:bedtools2"
        maxForks = 4
    }
    $BuildHostIndex {
        container = "mbull/bioinformatics-containers:bwa"
        maxForks = 1
    }
    $RunMultiQC {
        container = "cdeanj/auir:multiqc"
        maxForks = 4
    }
    $PreparePHEnixRef {
        container = "mbull/bioinformatics-containers:phenix"
        maxForks = 4
    }
    $PHEnixVariants {
        container = "mbull/bioinformatics-containers:phenix"
        maxForks = 4
    }
    $PHEnixVariantsToFasta {
        container = "mbull/bioinformatics-containers:phenix"
        maxForks = 4
    }
    $RemoveHostDNA {
        container = "mbull/bioinformatics-containers:samtools"
        maxForks = 4
    }
    $RunFastQC {
        container = "mbull/bioinformatics-containers:fastqc"
        maxForks = 4
    }
    $RunTrim {
        container = "mbull/bioinformatics-containers:trim-galore"
        maxForks = 4
    }
}