Segment-Flow/nextflow.config at master · FrancisCrickInstitute/Segment-Flow · GitHub

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manifest {
    name            = 'FrancisCrickInstitute/Segment-Flow'
    contributors = [
        [
            name: "Cameron Shand",
            email: "[email protected]"
        ],
        [
            name: "Numan Ahmed",
            email: "[email protected]"
        ],
        [
            name: "Fiona Young",
            email: "[email protected]"
        ],
        [
            name: "Qin Yu",
            email: "[email protected]"
        ],
        [
            name: "Jon Smith",
            email: "[email protected]"
        ]
    ]
    description     = 'Nextflow pipeline for deep learning segmentation models'
    homePage        = 'https://github.com/FrancisCrickInstitute/Segment-Flow'
    docsUrl         = 'https://franciscrickinstitute.github.io/aiod_docs/'
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    version         = '0.1.0'
}

process.container = 'quay.io/nextflow/bash'

nextflow.enable.moduleBinaries = true

conda.enabled = true

params {
    // General parameters
    help = false
    root_dir = "${System.getProperty('user.home')}/.nextflow/aiod"
    // Input csv specifying image filepaths and some basic dim info
    img_dir = null
    // General hashing param, used in mask saving in AIoD cache (root_dir)
    // If null, calcs a hash using params block
    // NOTE: This will be different from the hash that Napari calculates!!
    param_hash = null
    // Preprocessing parameters
    preprocess = null
    // Substack parameters
    num_substacks = "auto,auto,auto"
    overlap = "0.0,0.0,0.0"
    // Model parameters
    // NOTE: Defaults here just so that a user can "hello world"-style run the pipeline
    model = "cellpose"
    model_type = "cyto3"
    task = "cyto"
    model_config = null
    // Postprocessing parameters
    postprocess = false
    iou_threshold = 0.8
    // Output parameters
    output_format = "rle"
    output_mask_type = "auto"
}

profiles {
    crick { includeConfig 'profiles/crick.conf' }
    crick_dev { includeConfig 'profiles/crick_dev.conf' }
    local { includeConfig 'profiles/local.conf' }
    rosalind { includeConfig 'profiles/rosalind.conf' }
}

env {
    PYTHONNOUSERSITE = 'true'
}