{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "filter_with_counts",
  "description": "Filter scRNA-seq data based on the primary QC metrics. \nThis is based on both the UMI counts, the gene counts \nand the mitochondrial genes (genes starting with mt/MT).\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input h5mu file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
        },
        "modality": {
          "type": "string",
          "description": "Which modality from the input MuData file to process.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
          "default": "rna"
        },
        "layer": {
          "type": "string",
          "description": "Location of the count matrix",
          "help_text": "Type: `string`, multiple: `False`, example: `\"raw_counts\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output h5mu file.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "do_subset": {
          "type": "boolean",
          "description": "Whether to subset before storing the output.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "obs_name_filter": {
          "type": "string",
          "description": "In which .obs slot to store a boolean array corresponding to which observations should be removed.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"filter_with_counts\"`. ",
          "default": "filter_with_counts"
        },
        "var_name_filter": {
          "type": "string",
          "description": "In which .var slot to store a boolean array corresponding to which variables should be removed.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"filter_with_counts\"`. ",
          "default": "filter_with_counts"
        },
        "output_compression": {
          "type": "string",
          "description": "Compression format to use for the output AnnData and/or Mudata H5 files.\nBy default no compression is applied.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
          "enum": [
            "gzip",
            "lzf"
          ]
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "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_genes_per_cell": {
          "type": "integer",
          "description": "Minimum of non-zero values per cell.",
          "help_text": "Type: `integer`, multiple: `False`, example: `200`. "
        },
        "max_genes_per_cell": {
          "type": "integer",
          "description": "Maximum of non-zero values per cell.",
          "help_text": "Type: `integer`, multiple: `False`, example: `1500000`. "
        },
        "min_cells_per_gene": {
          "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/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
