nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/WEHI-SODA-Hub/sp_segment/master/nextflow_schema.json",
    "title": "WEHI-SODA-Hub/sp_segment pipeline parameters",
    "description": "Cell segmentation and downstream analysis pipeline for the COMET, MIBI, and OPAL spatial platforms",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.(csv|y(a)?ml)$",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://github.com/WEHI-SODA-Hub/sp_segment/blob/main/docs/usage.md).",
                    "fa_icon": "fas fa-file-csv"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                }
            }
        },
        "background_subtract_options": {
            "title": "Background subtraction options",
            "type": "object",
            "fa_icon": "fas fa-adjust",
            "description": "Parameters used for background subtraction.",
            "properties": {
                "remove_markers": {
                    "type": "string",
                    "description": "Comma-separated list of marker channels to remove from the background subtracted image. Note the channel name must match exactly (it is case sensitive).",
                    "fa_icon": "fas fa-eraser"
                }
            }
        },
        "combine_channel_options": {
            "title": "Combine options",
            "type": "object",
            "fa_icon": "fas fa-object-group",
            "description": "Parameters used for combining membrane channels.",
            "properties": {
                "combine_method": {
                    "type": "string",
                    "description": "Method used to combine membrane channels (product or max). Using product is not recommended for large numbers of channels with large images as this may use a lot of memory.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "enum": ["prod", "max"]
                }
            }
        },
        "sopa_options": {
            "title": "SOPA options",
            "type": "object",
            "fa_icon": "fas fa-microscope",
            "description": "Parameters used by SOPA for image patching.",
            "properties": {
                "technology": {
                    "type": "string",
                    "description": "Technology used for the imaging. Currently, only COMET is supported via the 'ome_tif' parameter.",
                    "fa_icon": "fas fa-microscope",
                    "enum": ["ome_tif"]
                },
                "patch_width_pixel": {
                    "type": "integer",
                    "description": "Width of patches in pixels.",
                    "fa_icon": "fas fa-crop"
                },
                "patch_overlap_pixel": {
                    "type": "integer",
                    "description": "Pixel overlap of patches. This should be set to at least the size of the largest cell in the image to ensure that cells are not split across patches.",
                    "fa_icon": "fas fa-crop"
                }
            }
        },
        "cellpose_options": {
            "title": "Cellpose options",
            "type": "object",
            "fa_icon": "fas fa-vial",
            "description": "Parameters used by Cellpose for the cell segmentation.",
            "properties": {
                "cellpose_diameter": {
                    "type": "integer",
                    "description": "Diameter of cells in pixels for cellpose.",
                    "fa_icon": "fas fa-circle"
                },
                "cellpose_min_area": {
                    "type": "number",
                    "description": "Minimum area of cells in square pixels for cellpose.",
                    "fa_icon": "fas fa-arrows-alt"
                },
                "cellpose_flow_threshold": {
                    "type": "number",
                    "description": "Flow threshold for cellpose.",
                    "fa_icon": "fas fa-tachometer-alt"
                },
                "cellpose_cellprob_threshold": {
                    "type": "number",
                    "description": "Cell probability threshold for cellpose.",
                    "fa_icon": "fas fa-check-circle"
                },
                "cellpose_model_type": {
                    "type": "string",
                    "description": "Cellpose model to use for segmentation (e.g. nuclei, cyto, cyto2, cyto3 etc.).",
                    "fa_icon": "fas fa-cogs"
                },
                "cellpose_pretrained_model": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Path to a pre-trained Cellpose model.",
                    "fa_icon": "fas fa-file-upload"
                }
            }
        },
        "mesmer_options": {
            "title": "Mesmer options",
            "type": "object",
            "fa_icon": "fas fa-vial",
            "description": "Parameters used by the MesmerSegmentation tool.",
            "properties": {
                "mesmer_segmentation_level": {
                    "type": "integer",
                    "description": "Segmentation level (legacy parameter).",
                    "fa_icon": "fas fa-layer-group",
                    "minimum": 0,
                    "maximum": 10
                },
                "mesmer_maxima_threshold": {
                    "type": "number",
                    "description": "Controls segmentation level directly in mesmer, (lower values = more cells, higher values = fewer cells). ",
                    "fa_icon": "fas fa-tachometer-alt",
                    "minimum": 0
                },
                "mesmer_interior_threshold": {
                    "type": "number",
                    "description": "Controls how conservative model is in distinguishing cell from background (higher values = more conservative interior therefore smaller nuclei & cells).",
                    "fa_icon": "fas fa-tachometer-alt"
                },
                "mesmer_maxima_smooth": {
                    "type": "number",
                    "description": "Smooths signal peaks (higher values = less irregular shapes/nuclei).",
                    "fa_icon": "fas fa-tachometer-alt",
                    "minimum": 0
                },
                "mesmer_min_nuclei_area": {
                    "type": "number",
                    "description": "Minimum area of nuclei to keep in square pixels.",
                    "fa_icon": "fas fa-arrows-alt",
                    "minimum": 0
                },
                "mesmer_remove_border_cells": {
                    "type": "boolean",
                    "description": "Remove cells that touch the image border.",
                    "fa_icon": "fas fa-border-all"
                },
                "mesmer_pixel_expansion": {
                    "type": "integer",
                    "description": "Manual pixel expansion after segmentation.",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "minimum": 0
                },
                "mesmer_padding": {
                    "type": "integer",
                    "description": "Number of pixels to crop the image by on each side before segmentation.",
                    "fa_icon": "fas fa-crop",
                    "minimum": 0
                },
                "mesmer_transpose_mask": {
                    "type": "boolean",
                    "default": false,
                    "description": "Force-transpose the Mesmer output mask. Enable this if the segmentation result appears spatially flipped relative to the input image.",
                    "fa_icon": "fas fa-exchange-alt"
                }
            }
        },
        "cellsam_options": {
            "title": "CellSAM options",
            "type": "object",
            "fa_icon": "fas fa-brain",
            "description": "Parameters used by CellSAM for foundation model cell segmentation.",
            "properties": {
                "cellsam_bbox_threshold": {
                    "type": "number",
                    "default": 0.4,
                    "description": "Confidence threshold for cell detection. Lower values (0.3-0.4) increase recall for out-of-distribution images.",
                    "fa_icon": "fas fa-tachometer-alt",
                    "minimum": 0.0,
                    "maximum": 1.0
                },
                "cellsam_block_size": {
                    "type": "integer",
                    "default": 600,
                    "description": "Tile size for large image processing. Recommended: 256-512 for dense images, 400-600 for sparse.",
                    "fa_icon": "fas fa-th",
                    "minimum": 128,
                    "maximum": 2048
                },  
                "cellsam_overlap": {
                    "type": "integer",
                    "default": 250,
                    "description": "Tile overlap region in pixels. Should encompass typical cell size for proper merging.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "minimum": 0,
                    "maximum": 256
                },
                "cellsam_iou_depth": {
                    "type": "integer",
                    "default": 250,
                    "description": "Depth for IOU-based label merging across tiles. 250 works well for COMET images.",
                    "fa_icon": "fas fa-layer-group",
                    "minimum": 0,
                    "maximum": 256
                },
                "cellsam_iou_threshold": {
                    "type": "number",
                    "default": 0.5,
                    "description": "IOU threshold for merging overlapping labels across tiles.",
                    "fa_icon": "fas fa-project-diagram",
                    "minimum": 0.0,
                    "maximum": 1.0
                },
                "cellsam_use_wsi": {
                    "type": "boolean",
                    "default": true,
                    "description": "Enable tiling for large images. Recommended for images with >3000 cells.",
                    "fa_icon": "fas fa-th-large"
                },
                "cellsam_gauge_cell_size": {
                    "type": "boolean",
                    "default": false,
                    "description": "Perform preliminary segmentation to estimate cell sizes.",
                    "fa_icon": "fas fa-ruler-combined"
                },
                "cellsam_low_contrast_enhancement": {
                    "type": "boolean",
                    "default": false,
                    "description": "Apply contrast enhancement preprocessing for low-contrast images.",
                    "fa_icon": "fas fa-adjust"
                },
                "cellsam_model_path": {
                    "type": "string",
                    "description": "Path to custom CellSAM model weights. If not specified, uses latest generalist model (v1.2 with DEEPCELL_ACCESS_TOKEN).",
                    "fa_icon": "fas fa-file-medical",
                    "format": "file-path"
                },
                "cellsam_min_area": {
                    "type": "integer",
                    "default": 0,
                    "description": "Minimum area in pixels for cells/nuclei. Segmented objects smaller than this are removed. Set to 0 to disable.",
                    "fa_icon": "fas fa-compress-arrows-alt"
                }
            }
        },
        "kronos_options": {
            "title": "KRONOS options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "Parameters for KRONOS foundation model cell embedding extraction.",
            "help_text": "KRONOS is a foundation model for multiplex spatial proteomic images. These parameters control the embedding extraction step that runs after cell measurement.",
            "properties": {
                "skip_kronos": {
                    "type": "boolean",
                    "default": true,
                    "description": "Skip KRONOS embedding extraction step.",
                    "fa_icon": "fas fa-stopwatch",
                    "help_text": "Set this to `false` to run KRONOS embedding extraction after cell measurement. Requires kronos_model_path and kronos_marker_metadata to be set."
                },
                "kronos_model_path": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to directory containing KRONOS model weights (.pt file) and config.json.",
                    "fa_icon": "fas fa-file-medical",
                    "help_text": "The directory should contain the model checkpoint (e.g. kronos_vits16_model.pt) and optionally a config.json file. Download from https://github.com/mahmoodlab/KRONOS or Hugging Face Hub (MahmoodLab/kronos)."
                },
                "kronos_marker_metadata": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Path to KRONOS marker metadata CSV file with columns: marker_name, marker_id, marker_mean, marker_std.",
                    "fa_icon": "fas fa-file-csv",
                    "help_text": "This CSV maps marker names to KRONOS internal marker IDs and provides normalization statistics. A default metadata file is provided with the KRONOS repository. KRONOS uses fuzzy string matching to match image channel names to the metadata, but exact matches are preferred."
                },
                "kronos_patch_size": {
                    "type": "integer",
                    "default": 64,
                    "description": "Size of cell-centered patches to extract for KRONOS inference.",
                    "fa_icon": "fas fa-crop",
                    "minimum": 16,
                    "maximum": 256,
                    "help_text": "The patch size in pixels for cell-centered crops. Larger patches capture more context but increase computation. Typical values are 32-128."
                },
                "kronos_batch_size": {
                    "type": "integer",
                    "default": 32,
                    "description": "Batch size for KRONOS model inference.",
                    "fa_icon": "fas fa-layer-group",
                    "minimum": 1,
                    "maximum": 512,
                    "help_text": "Number of cell patches to process simultaneously. Larger batch sizes are faster but require more GPU memory."
                },
                "kronos_num_workers": {
                    "type": "integer",
                    "default": 4,
                    "description": "Number of parallel DataLoader workers for loading and preprocessing cell patches.",
                    "fa_icon": "fas fa-cogs",
                    "minimum": 0,
                    "maximum": 32,
                    "help_text": "Controls how many CPU processes load and preprocess patches in parallel while the GPU runs inference. Set to 0 for single-process loading (useful for debugging). On HPC, set this to match the number of CPUs allocated to the KRONOS job for best throughput."
                },
                "kronos_max_value": {
                    "type": "number",
                    "default": 65535,
                    "description": "Maximum intensity value for image normalization (65535 for 16-bit images).",
                    "fa_icon": "fas fa-sliders-h",
                    "minimum": 1,
                    "help_text": "Used to scale raw pixel intensities before applying KRONOS normalization. Use 65535 for 16-bit images, 255 for 8-bit."
                },
                "kronos_marker_mapping": {
                    "type": "string",
                    "description": "JSON string mapping image marker names to KRONOS marker names for markers that cannot be auto-matched.",
                    "fa_icon": "fas fa-exchange-alt",
                    "help_text": "Provide a JSON string like '{\"CD3e\": \"CD3E\", \"PanCK\": \"PANCK\"}' to manually resolve marker name mismatches between your image channels and the KRONOS metadata. KRONOS performs case-insensitive matching automatically, so only provide mappings for markers that truly differ in name."
                }
            }
        },
        "mask_smoothing_options": {
            "title": "Mask smoothing options",
            "type": "object",
            "fa_icon": "fas fa-magic",
            "description": "Parameters for optional mask smoothing before cell measurement.",
            "help_text": "Enable mask smoothing to reduce polygon complexity in segmentation masks. This can prevent StackOverflowError in QuPath's GeoJSON export when cell ROIs have overly complex/jagged boundaries.",
            "properties": {
                "smooth_masks": {
                    "type": "boolean",
                    "default": false,
                    "description": "Enable mask smoothing before cell measurement.",
                    "fa_icon": "fas fa-wave-square",
                    "help_text": "When enabled, segmentation masks are smoothed to reduce polygon complexity before being passed to cellmeasurement. Choose the method with smooth_method."
                },
                "smooth_method": {
                    "type": "string",
                    "default": "morphological",
                    "description": "Smoothing algorithm: 'morphological' (disk close+open) or 'shapely' (Douglas-Peucker polygon simplification).",
                    "fa_icon": "fas fa-cogs",
                    "enum": ["morphological", "shapely"],
                    "help_text": "'morphological' applies binary close then open with a disk kernel to smooth pixel boundaries. 'shapely' extracts the polygon boundary for each label and applies Shapely's simplify (Douglas-Peucker) algorithm, which directly reduces vertex count — the main cause of StackOverflowError in QuPath GeoJSON export."
                },
                "smooth_kernel_size": {
                    "type": "integer",
                    "default": 2,
                    "minimum": 1,
                    "maximum": 10,
                    "description": "Disk radius for morphological close+open smoothing (pixels).",
                    "fa_icon": "fas fa-circle",
                    "help_text": "Larger values produce smoother boundaries but may merge nearby cells. Only used when smooth_masks is enabled."
                },
                "smooth_n_workers": {
                    "type": "integer",
                    "default": 8,
                    "minimum": 1,
                    "maximum": 64,
                    "description": "Number of parallel worker processes for smoothing.",
                    "fa_icon": "fas fa-tasks",
                    "help_text": "Set to match available CPUs for optimal performance. Should match --cpus-per-task in your resource configuration"
                },
                "smooth_chunksize": {
                    "type": "integer",
                    "default": 200,
                    "minimum": 1,
                    "maximum": 10000,
                    "description": "Number of labels per worker chunk.",
                    "fa_icon": "fas fa-layer-group",
                    "help_text": "Tune based on cell size distribution. Larger values for many small cells, smaller values for fewer large cells."
                },
                "smooth_tolerance": {
                    "type": "number",
                    "default": 1,
                    "minimum": 0.01,
                    "description": "[shapely] Douglas-Peucker simplification tolerance in pixels.",
                    "fa_icon": "fas fa-sliders-h",
                    "help_text": "Controls how aggressively polygon boundaries are simplified when smooth_method is 'shapely'. Higher values produce simpler (fewer vertex) polygons but less accurate boundaries. Important to minimise vertex count to prevent StackOverflowError in QuPath GeoJSON export. Tune based on typical cell size and boundary complexity. Start with threshold 1 and adjust as needed."
                },
                "smooth_min_area": {
                    "type": "number",
                    "default": 0,
                    "minimum": 0,
                    "description": "[shapely] Minimum polygon area in pixels² to retain after simplification.",
                    "fa_icon": "fas fa-compress-arrows-alt",
                    "help_text": "Labels whose simplified polygon area falls below this threshold are removed from the output mask. Useful for discarding fragments created by aggressive simplification. Only used when smooth_method is 'shapely'."
                }
            }
        },
        "measurement_options": {
            "title": "Cell measurement options",
            "type": "object",
            "fa_icon": "fas fa-image",
            "description": "Parameters used for cell measurement.",
            "help_text": "These parameters controls parameters used by the cellmeasurement step of the pipeline.",
            "properties": {
                "skip_measurements": {
                    "type": "boolean",
                    "default": false,
                    "description": "Skip cell measurement step.",
                    "fa_icon": "fas fa-stopwatch",
                    "help_text": "Set this to `true` to skip the cell measurement step of the pipeline. Nuclei and whole-cells will still be merged but compartment metrics will not be calculated (this can save processing time)."
                },
                "percentiles": {
                    "type": "string",
                    "default": "70,80,90,95,99",
                    "description": "Comma-separated list of percentiles to calculate for each marker (e.g. 80,90,95,99).",
                    "fa_icon": "fas fa-percentage",
                    "pattern": "^(100|[1-9]?[0-9][\\.]?[0-9]*)(,(100|[1-9]?[0-9][\\.]?[0-9]*))*$",
                    "help_text": "A comma-separated list of percentiles to calculate for each marker. Each value must be between 0 and 100. Default: 70,80,90,95,99. Skip measurements must be set to `false` to use this parameter."
                },
                "erosion_steps": {
                    "type": "boolean",
                    "default": true,
                    "description": "Measure intensity in 5 equal-area erosion bins working inward from the cell/nucleus boundary.",
                    "fa_icon": "fas fa-ruler-combined",
                    "help_text": "Divides each cell and nucleus mask into 5 concentric zones of approximately equal area by iterative morphological erosion, then measures mean/median intensity per zone. Adapts automatically to cell size. Set to false to disable. Skip measurements must be set to false to use this parameter."
                },
                "expansion_steps": {
                    "type": "boolean",
                    "default": true,
                    "description": "Measure intensity in 5 equal-area annular bins dilated 20 µm outward from the cell boundary (distance computed from pixel_size_microns).",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "help_text": "Divides the 20 µm pericellular zone into 5 rings of approximately equal area and measures mean/median intensity per ring. The total expansion distance is computed automatically from pixel_size_microns. Set to false to disable. Skip measurements must be set to false to use this parameter."
                },
                "environment_expansion": {
                    "type": "boolean",
                    "default": true,
                    "description": "Measure a 20 µm pericellular 'Environment' compartment (distance computed automatically from pixel_size_microns).",
                    "fa_icon": "fas fa-circle-notch",
                    "help_text": "Dilates the cell mask by 20 µm (converted to pixels via pixel_size_microns) and measures mean, median, min, max, and std dev of every channel in the full zone (cell boundary to outer ring) as one region. This matches CellTune's 'Environment' compartment. Set to false to disable."
                },
                "pixel_size_microns": {
                    "type": "number",
                    "description": "Pixel size in microns.",
                    "minimum": 0.1,
                    "maximum": 10.0,
                    "fa_icon": "fas fa-ruler-combined",
                    "help_text": "COMET: 0.28 µm/px, MIBI: 0.390625 µm/px, OPAL: 0.4964 µm/px."
                },
                "estimate_cell_boundary_dist": {
                    "type": "integer",
                    "description": "Where no matching membrane ROI exists, expand the nucleus by this many pixels (default = 3.0).",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "minimum": 0
                },
                "skip_nuclear_mask": {
                    "type": "boolean",
                    "default": false,
                    "description": "Ignore the nuclear mask and generate ROIs from the whole-cell mask only. Skips compartmental measurements (Nucleus, Cytoplasm, Membrane) but retains Cell, erosion, and expansion measurements.",
                    "fa_icon": "fas fa-ban"
                },
                "neighbors": {
                    "type": "integer",
                    "default": 5,
                    "minimum": 0,
                    "description": "Number of nearest neighbors for neighborhood feature aggregation (0 = disabled).",
                    "fa_icon": "fas fa-project-diagram",
                    "help_text": "For each cell, the max and mean of every numeric measurement are computed across its k closest spatial neighbours (by centroid distance). This produces features like 'Neighbors: Max: CD3: Cell: Mean' and 'Neighbors: Mean: CD3: Cell: Mean'. Set to 0 to disable. Typical values: 5\u201310."
                },
                "gzip_geojson": {
                    "type": "boolean",
                    "default": false,
                    "description": "Gzip-compress the output GeoJSON files. Produces .geojson.gz instead of .geojson.",
                    "fa_icon": "fas fa-file-archive",
                    "help_text": "Enable this to gzip-compress the GeoJSON output from cellmeasurement. For large images with hundreds of thousands of cells, the GeoJSON can be 100+ GB uncompressed. Gzip typically achieves 10-20x compression on JSON with floating-point coordinates. The compressed files can be used directly with the import_large_geojson pipeline."
                }
            }
        },
        "report_options": {
            "title": "Report options",
            "type": "object",
            "fa_icon": "fas fa-image",
            "description": "Parameters used for segmentation report generation.",
            "help_text": "These parameters controls parameters used by the segmentationreport step of the pipeline.",
            "properties": {
                "generate_report": {
                    "type": "boolean",
                    "default": true,
                    "description": "Generate segmentation report.",
                    "fa_icon": "fas fa-stopwatch",
                    "help_text": "Set this to `true` to generate a segmentation report. It is recommended that skip_measurements is set to `false` for the most comprehensive report. Skipping this step can save on processing time."
                }
            }
        },
        "institutional_config_options": {
            "title": "Institutional config options",
            "type": "object",
            "fa_icon": "fas fa-university",
            "description": "Parameters used to describe centralised config profiles. These should not be edited.",
            "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
            "properties": {
                "custom_config_version": {
                    "type": "string",
                    "description": "Git commit id for Institutional configs.",
                    "default": "master",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "custom_config_base": {
                    "type": "string",
                    "description": "Base directory for Institutional configs.",
                    "default": "https://raw.githubusercontent.com/nf-core/configs/master",
                    "hidden": true,
                    "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_name": {
                    "type": "string",
                    "description": "Institutional config name.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_description": {
                    "type": "string",
                    "description": "Institutional config description.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_contact": {
                    "type": "string",
                    "description": "Institutional config contact information.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_url": {
                    "type": "string",
                    "description": "Institutional config URL link.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                }
            }
        },
        "generic_options": {
            "title": "Generic options",
            "type": "object",
            "fa_icon": "fas fa-file-import",
            "description": "Less common options for the pipeline, typically set in a config file.",
            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
            "properties": {
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "description": "Method used to save pipeline results to output directory.",
                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                    "fa_icon": "fas fa-copy",
                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                    "hidden": true
                },
                "email_on_fail": {
                    "type": "string",
                    "description": "Email address for completion summary, only when pipeline fails.",
                    "fa_icon": "fas fa-exclamation-triangle",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
                    "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
                    "hidden": true
                },
                "plaintext_email": {
                    "type": "boolean",
                    "description": "Send plain-text email instead of HTML.",
                    "fa_icon": "fas fa-remove-format",
                    "hidden": true
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming hook URL for messaging service",
                    "fa_icon": "fas fa-people-group",
                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                    "hidden": true
                },
                "validate_params": {
                    "type": "boolean",
                    "description": "Boolean whether to validate parameters against the schema at runtime",
                    "default": true,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "pipelines_testdata_base_path": {
                    "type": "string",
                    "fa_icon": "far fa-check-circle",
                    "description": "Base URL or local path to location of pipeline test dataset files",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                    "hidden": true
                },
                "gradle_cache_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Directory to use for Gradle cache.",
                    "fa_icon": "fas fa-cogs",
                    "hidden": true
                },
                "deepcell_cache_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "default": "/vast/scratch/users",
                    "description": "Base directory for caching DeepCell/CellSAM model weights. The current username is appended automatically.",
                    "fa_icon": "fas fa-database",
                    "help_text": "Set this to redirect the DeepCell model cache away from the home directory. The current username is resolved at runtime and appended, so models are cached at {deepcell_cache_dir}/{username}/.deepcell/models/. Set to null to use $HOME instead."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/background_subtract_options"
        },
        {
            "$ref": "#/$defs/combine_channel_options"
        },
        {
            "$ref": "#/$defs/sopa_options"
        },
        {
            "$ref": "#/$defs/cellpose_options"
        },
        {
            "$ref": "#/$defs/mesmer_options"
        },
        {
            "$ref": "#/$defs/cellsam_options"
        },
        {
            "$ref": "#/$defs/kronos_options"
        },
        {
            "$ref": "#/$defs/mask_smoothing_options"
        },
        {
            "$ref": "#/$defs/measurement_options"
        },
        {
            "$ref": "#/$defs/report_options"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}