{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "listInputDir",
  "description": "List the contents of a directory and parse contained fastq files",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to the directory containing fastq files",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"fastq_dir\"`. "
        },
        "ignore": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Pool names to ignore.",
          "help_text": "Type: `string`, multiple: `True`, default: `[\"Undetermined\"]`. ",
          "default": [
            "Undetermined"
          ]
        },
        "r1_output": {
          "type": "string",
          "format": "path",
          "description": "Path to read 1 fastq/fasta file",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.r1_output\"`, direction: `output`. ",
          "default": "$id.$key.r1_output"
        },
        "r2_output": {
          "type": "string",
          "format": "path",
          "description": "Path to read 2 fastq/fasta file",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.r2_output\"`, direction: `output`. ",
          "default": "$id.$key.r2_output"
        },
        "lane": {
          "type": "string",
          "description": "Lane nr",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "sample": {
          "type": "string",
          "description": "Sample nr",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "sample_id": {
          "type": "string",
          "description": "Sample name",
          "help_text": "Type: `string`, multiple: `False`. "
        }
      }
    },
    "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/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
