{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "prot_singlesample",
  "description": "Processing unimodal single-sample CITE-seq data.",
  "type": "object",
  "$defs": {
    "input": {
      "title": "Input",
      "type": "object",
      "description": "No description",
      "properties": {
        "id": {
          "type": "string",
          "description": "ID of the sample.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"foo\"`. "
        },
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to the sample.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"dataset.h5mu\"`. "
        },
        "layer": {
          "type": "string",
          "description": "Input layer to start from",
          "help_text": "Type: `string`, multiple: `False`. "
        }
      }
    },
    "output": {
      "title": "Output",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Destination path to the output.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        }
      }
    },
    "filtering options": {
      "title": "Filtering options",
      "type": "object",
      "description": "No description",
      "properties": {
        "min_counts": {
          "type": "integer",
          "description": "Minimum number of counts captured per cell.",
          "help_text": "Type: `integer`, multiple: `False`, example: `200`. "
        },
        "max_counts": {
          "type": "integer",
          "description": "Maximum number of counts captured per cell.",
          "help_text": "Type: `integer`, multiple: `False`, example: `5000000`. "
        },
        "min_percentile_counts": {
          "type": "number",
          "description": "Minimum percentile of total protein counts captured per cell",
          "help_text": "Type: `double`, multiple: `False`, example: `0.05`. "
        },
        "max_percentile_counts": {
          "type": "number",
          "description": "Maximum percentile of total protein counts captured per cell",
          "help_text": "Type: `double`, multiple: `False`, example: `0.95`. "
        },
        "min_proteins_per_cell": {
          "type": "integer",
          "description": "Minimum of non-zero values per cell.",
          "help_text": "Type: `integer`, multiple: `False`, example: `200`. "
        },
        "max_proteins_per_cell": {
          "type": "integer",
          "description": "Maximum of non-zero values per cell.",
          "help_text": "Type: `integer`, multiple: `False`, example: `1500000`. "
        },
        "min_cells_per_protein": {
          "type": "integer",
          "description": "Minimum of non-zero values per gene.",
          "help_text": "Type: `integer`, multiple: `False`, example: `3`. "
        }
      }
    },
    "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/input"
    },
    {
      "$ref": "#/$defs/output"
    },
    {
      "$ref": "#/$defs/filtering options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
