{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "star_genome_generate",
  "description": "Create index for STAR\n",
  "type": "object",
  "$defs": {
    "input": {
      "title": "Input",
      "type": "object",
      "description": "No description",
      "properties": {
        "genome_fasta_files": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Path(s) to the fasta files with the genome sequences, separated by spaces",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
        },
        "sjdb_gtf_file": {
          "type": "string",
          "format": "path",
          "description": "Path to the GTF file with annotations",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "sjdb_overhang": {
          "type": "integer",
          "description": "Length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)",
          "help_text": "Type: `integer`, multiple: `False`, example: `100`. "
        },
        "sjdb_gtf_chr_prefix": {
          "type": "string",
          "description": "Prefix for chromosome names in a GTF file (e.g",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "sjdb_gtf_feature_exon": {
          "type": "string",
          "description": "Feature type in GTF file to be used as exons for building transcripts",
          "help_text": "Type: `string`, multiple: `False`, example: `\"exon\"`. "
        },
        "sjdb_gtf_tag_exon_parent_transcript": {
          "type": "string",
          "description": "GTF attribute name for parent transcript ID (default \"transcript_id\" works for GTF files)",
          "help_text": "Type: `string`, multiple: `False`, example: `\"transcript_id\"`. "
        },
        "sjdb_gtf_tag_exon_parent_gene": {
          "type": "string",
          "description": "GTF attribute name for parent gene ID (default \"gene_id\" works for GTF files)",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gene_id\"`. "
        },
        "sjdb_gtf_tag_exon_parent_gene_name": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "GTF attribute name for parent gene name",
          "help_text": "Type: `string`, multiple: `True`, example: `[\"gene_name\"]`. "
        },
        "sjdb_gtf_tag_exon_parent_gene_type": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "GTF attribute name for parent gene type",
          "help_text": "Type: `string`, multiple: `True`, example: `[\"gene_type\";\"gene_biotype\"]`. "
        },
        "limit_genome_generate_ram": {
          "type": "string",
          "description": "Maximum available RAM (bytes) for genome generation",
          "help_text": "Type: `long`, multiple: `False`, example: `31000000000`. "
        },
        "genome_sa_index_nbases": {
          "type": "integer",
          "description": "Length (bases) of the SA pre-indexing string",
          "help_text": "Type: `integer`, multiple: `False`, example: `14`. "
        },
        "genome_chr_bin_nbits": {
          "type": "integer",
          "description": "Defined as log2(chrBin), where chrBin is the size of the bins for genome storage",
          "help_text": "Type: `integer`, multiple: `False`, example: `18`. "
        },
        "genome_sa_sparse_d": {
          "type": "integer",
          "description": "Suffux array sparsity, i.e",
          "help_text": "Type: `integer`, multiple: `False`, example: `1`. "
        },
        "genome_suffix_length_max": {
          "type": "integer",
          "description": "Maximum length of the suffixes, has to be longer than read length",
          "help_text": "Type: `integer`, multiple: `False`, example: `-1`. "
        },
        "genome_transform_type": {
          "type": "string",
          "description": "Type of genome transformation\n  None       ..",
          "help_text": "Type: `string`, multiple: `False`, example: `\"None\"`. "
        },
        "genome_transform_vcf": {
          "type": "string",
          "format": "path",
          "description": "path to VCF file for genome transformation",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        }
      }
    },
    "output": {
      "title": "Output",
      "type": "object",
      "description": "No description",
      "properties": {
        "index": {
          "type": "string",
          "format": "path",
          "description": "STAR index directory.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"STAR_index\"`, direction: `output`. ",
          "default": "STAR_index"
        }
      }
    },
    "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/nextflow input-output arguments"
    }
  ]
}
