{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "filter_with_pattern",
  "description": "Filter a MuData object based on gene names using a regex.\n",
  "type": "object",
  "$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"
        },
        "var_gene_names": {
          "type": "string",
          "description": "The .var field containing the gene names to be filtered",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gene_symbol\"`. "
        },
        "pattern": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "A regex pattern to filter the gene names.\n",
          "help_text": "Type: `string`, multiple: `True`, required, example: `[\"MIR\\d+\";\"AL\\d+\";\"LINC\\d+\";\"AC\\d+\";\"AP\\d+\"]`. "
        }
      }
    },
    "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
        },
        "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_pattern\"`. ",
          "default": "filter_with_pattern"
        },
        "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"
          ]
        }
      }
    },
    "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/nextflow input-output arguments"
    }
  ]
}
