nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/nf-artist/dsl2/nextflow_schema.json",
    "title": "Sage-Bionetworks-Workflows/nf-artist parameters",
    "description": "Nextflow pipeline for generating Minerva stories and Miniature thumbnails from multiplexed tissue imaging datasets",
    "type": "object",
    "definitions": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
           "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/csv",
                    "description": "Path to a CSV samplesheet"
                },
                "outdir": {
                    "type": "string",
                    "description": "Directory in which outputs are placed",
                    "default": "outputs"
                }
            }
        },
        "miniatue_options": {
            "title": "Miniature options",
            "type": "object",
            "fa_icon": "fas fa-palette",
            "description": "Define HTAN Artist pipeline parameters.",
            "properties": {
                "remove_bg": {
                    "type": "boolean",
                    "description": "Remove non-tissue background",
                    "default": true
                },
                "level": {
                    "type": "integer",
                    "description": "The pyramid level used in thumbnauls, Default: -1 (smallest)",
                    "default": -1
                },
                "dimred": {
                    "type": "string",
                    "description": "The dimensionality reduction method used",
                    "default": "umap",
                    "enum": ["umap", "tsne", "pca"]
                },
                "colormap": {
                    "type": "string",
                    "description": "The colormap used. Ensure colormap is compatiable with `n_components` selected ",
                    "enum": ["UCIE", "LAB", "RGB", "BREMM", "SCHUMANN", "STEIGER", "TEULING2", "ZIEGLER","CUBEDIAGONAL"],
                    "default": "UCIE"
                },
                "n_components": {
                    "type": "integer",
                    "description": "",
                    "default": 3,
                    "enum": [2,3]
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/parameters"
        }
    ]
}