fractal-multistep-nextflow/nextflow.config at main · BioImageTools/fractal-multistep-nextflow · GitHub

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manifest {
    name            = 'fractal-multistep-nextflow'
    description     = 'Chaining several fractal-tasks-core tasks in one Nextflow workflow on OME-Zarr'
    author          = 'Tong LI'
    homePage        = 'https://github.com/BioImageTools/fractal-multistep-nextflow'
    license         = 'BSD-3-Clause'
    version         = '0.1.0'
    nextflowVersion = '>=24.04.0'
    mainScript      = 'main.nf'
}

params {
    // [ meta, path-to-OME-Zarr ]: an HCS plate (processed image by image) or a
    // single image. meta may also carry `channel` / `label_name`.
    // data/PLK1_plate.zarr is built by scripts/make_test_plate.py
    images = [
        [ [id: 'PLK1_plate'], "${projectDir}/data/PLK1_plate.zarr" ],
    ]
    out_dir = 'results'

    // Segmentation (fractal-tasks-core threshold_segmentation)
    channel_mode     = 'index'   // 'index' | 'label' | 'wavelength_id'
    channel          = '0'
    label_name       = 'nuclei'
    threshold_method = 'Otsu'    // 'Otsu' | 'Simple Threshold'
    threshold        = null      // used only when threshold_method = 'Simple Threshold'
    sigma_xy         = 2.5       // Gaussian blur pre-processing; null to disable
    min_size         = 20        // drop objects smaller than this (pixels); null to disable

    // Image with fractal-tasks-core installed (see containers/Dockerfile)
    fractal_container = 'quay.io/bioinfotongli/fractal-tasks-core:2.1.0'

    // Run-level provenance (-profile prov, see conf/prov.config)
    prov_license           = 'BSD-3-Clause'  // licence of the RO-Crate (the run's results); SPDX id or URL
    prov_agent_name        = null            // person running the pipeline
    prov_agent_orcid       = null            // e.g. 'https://orcid.org/0000-0000-0000-0000'
    prov_agent_email       = null
    prov_organization_name = null            // e.g. 'Wellcome Sanger Institute'
    prov_organization_ror  = null            // e.g. 'https://ror.org/05cy4wa09'
}

includeConfig 'conf/modules.config'

profiles {
    docker {
        docker.enabled = true
        // run as the calling user so files written into the OME-Zarr are not root-owned
        docker.runOptions = '-u $(id -u):$(id -g)'
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
    }
    conda {
        conda.enabled = true
    }
    wave {
        // build the container on the fly from each module's environment.yml
        docker.enabled = true
        docker.runOptions = '-u $(id -u):$(id -g)'
        wave.enabled   = true
        wave.strategy  = 'conda'
    }
    local {
        // use whatever `python` with fractal-tasks-core is already on PATH
    }
    prov {
        // nf-prov RO-Crate + BCO + DAG, and trace/report/timeline
        includeConfig 'conf/prov.config'
    }
}