{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "seqtk_subseq",
  "description": "Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a name.lst (sequence ids file) or a reg.bed (genomic regions file).\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "The input FASTA/Q file.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.fa\"`. "
        },
        "name_list": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "List of sequence names (name.lst) or genomic regions (reg.bed) to extract.\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"list.lst\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "The output FASTA/Q file.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"output.fa\"`, direction: `output`. ",
          "default": "output.fa"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "tab": {
          "type": "boolean",
          "description": "TAB delimited output.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "strand_aware": {
          "type": "boolean",
          "description": "Strand aware.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "sequence_line_length": {
          "type": "integer",
          "description": "Sequence line length of input fasta file",
          "help_text": "Type: `integer`, multiple: `False`, example: `0`. "
        }
      }
    },
    "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/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
