{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "scvelo",
  "description": "No description",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input MuData file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "counts_layer": {
          "type": "string",
          "description": "Name of the counts layer, if not specified, X is used.",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "modality": {
          "type": "string",
          "description": "Input modality",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "layer_spliced": {
          "type": "string",
          "description": "Name of the layer to store the spliced abundances in",
          "help_text": "Type: `string`, multiple: `False`, default: `\"spliced\"`. ",
          "default": "spliced"
        },
        "layer_unspliced": {
          "type": "string",
          "description": "Name of the layer to store the unspliced abundances in.\nWill be used as key in the .layer attribute of the output MuData object.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"unspliced\"`. ",
          "default": "unspliced"
        },
        "layer_ambiguous": {
          "type": "string",
          "description": "Name of the layer to store the abundances in for which no fate was determined.\nWill be used as key in the .layer attribute of the output MuData object.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"ambiguous\"`. ",
          "default": "ambiguous"
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output directory",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
          "default": "$id.$key.output"
        },
        "output_h5mu": {
          "type": "string",
          "format": "path",
          "description": "Output mudata file.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_h5mu\"`, direction: `output`. ",
          "default": "$id.$key.output_h5mu"
        },
        "output_compression": {
          "type": "string",
          "description": "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
          "enum": [
            "gzip",
            "lzf"
          ]
        }
      }
    },
    "filtering and normalization": {
      "title": "Filtering and normalization",
      "type": "object",
      "description": "Arguments for filtering, normalization an log transform (see scvelo.pp.filter_and_normalize function)",
      "properties": {
        "min_counts": {
          "type": "integer",
          "description": "Minimum number of counts required for a gene to pass filtering (spliced).",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "min_counts_u": {
          "type": "integer",
          "description": "Minimum number of counts required for a gene to pass filtering (unspliced).",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "min_cells": {
          "type": "integer",
          "description": "Minimum number of cells expressed required to pass filtering (spliced).",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "min_cells_u": {
          "type": "integer",
          "description": "Minimum number of cells expressed required to pass filtering (unspliced).",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "min_shared_counts": {
          "type": "integer",
          "description": "Minimum number of counts (both unspliced and spliced) required for a gene.",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "min_shared_cells": {
          "type": "integer",
          "description": "Minimum number of cells required to be expressed (both unspliced and spliced).",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "n_top_genes": {
          "type": "integer",
          "description": "Number of genes to keep.",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "log_transform": {
          "type": "boolean",
          "description": "Do not log transform counts.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        }
      }
    },
    "fitting parameters": {
      "title": "Fitting parameters",
      "type": "object",
      "description": "Arguments for fitting the data",
      "properties": {
        "n_principal_components": {
          "type": "integer",
          "description": "Number of principal components to use for calculating moments.",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "n_neighbors": {
          "type": "integer",
          "description": "Number of neighbors to use",
          "help_text": "Type: `integer`, multiple: `False`, default: `30`. ",
          "default": 30
        }
      }
    },
    "nextflow input-output arguments": {
      "title": "Nextflow input-output arguments",
      "type": "object",
      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
      "properties": {
        "publish_dir": {
          "type": "string",
          "description": "Path to an output directory.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/filtering and normalization"
    },
    {
      "$ref": "#/$defs/fitting parameters"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
