sramic/nextflow_schema.json at main · microbemarsh/sramic · GitHub

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{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://github.com/microbemarsh/sramic/nextflow_schema.json",
  "title": "sramic parameters",
  "type": "object",
  "properties": {
    "manifest": {"type": ["string", "null"], "format": "file-path"},
    "taxid": {
      "type": ["integer", "string", "null"],
      "description": "Positive NCBI Taxonomy ID used for metadata-first ENA discovery."
    },
    "taxon_id": {"type": ["integer", "string", "null"]},
    "taxon_name": {"type": ["string", "null"]},
    "outdir": {"type": "string", "default": "results"},
    "supplement_biosample": {"type": "boolean", "default": false},
    "metadata_cache": {"type": "string", "default": "work/cache/metadata"},
    "geography_validation": {"type": "string", "enum": ["none", "syntax", "country"], "default": "syntax"},
    "country_boundaries": {"type": ["string", "null"], "format": "file-path"},
    "ncbi_taxdump": {"type": ["string", "null"], "format": "directory-path"},
    "gtdb_mapping": {"type": ["string", "null"], "format": "file-path"},
    "min_metadata_score": {"type": "number", "minimum": 0, "maximum": 100, "default": 0},
    "min_geography_score": {"type": "number", "minimum": 0, "maximum": 35, "default": 0},
    "min_date_score": {"type": "number", "minimum": 0, "maximum": 20, "default": 0},
    "min_host_score": {"type": "number", "minimum": 0, "maximum": 20, "default": 0},
    "require_country": {"type": "boolean", "default": false},
    "require_coordinates": {"type": "boolean", "default": false},
    "require_collection_date": {"type": "boolean", "default": false},
    "require_host": {"type": "boolean", "default": false},
    "require_isolation_source": {"type": "boolean", "default": false},
    "library_strategy": {"type": ["string", "null"]},
    "library_source": {"type": ["string", "null"]},
    "library_selection": {"type": ["string", "null"]},
    "platform": {"type": ["string", "null"]},
    "instrument_model": {"type": ["string", "null"]},
    "collection_year_min": {"type": ["integer", "null"]},
    "collection_year_max": {"type": ["integer", "null"]},
    "country": {"type": ["string", "null"]},
    "host_tax_id": {"type": ["string", "integer", "null"]},
    "max_accessions": {"type": "integer", "minimum": 0, "default": 0},
    "threads": {
      "type": "integer",
      "minimum": 1,
      "default": 8,
      "description": "Total CPU/thread budget. Local tasks share this pool; sequence transfer and extraction can use the full budget."
    },
    "download_retries": {"type": "integer", "minimum": 0, "default": 3},
    "fetch_raw_reads": {"type": "boolean", "default": false},
    "download_sequences": {
      "type": "boolean",
      "default": false,
      "description": "Retrieve only metadata-selected runs through the selected download backend."
    },
    "download_backend": {
      "type": "string",
      "enum": ["kingfisher", "sracha"],
      "default": "kingfisher",
      "description": "Downloader for selected runs: Kingfisher source fallbacks or resumable sracha-rs download, decode, and compressed-FASTQ output."
    },
    "estimate_download_size": {
      "type": "boolean",
      "default": false,
      "description": "Annotate selected runs and report their aggregate archive transfer-size estimate without downloading sequence data."
    },
    "kingfisher_annotate": {
      "type": "boolean",
      "default": false,
      "description": "Annotate selected runs with Kingfisher even when sequence acquisition is disabled; acquisition enables annotation automatically."
    },
    "download_sra": {
      "type": "boolean",
      "default": false,
      "description": "Compatibility alias for --download_sequences."
    },
    "kingfisher_methods": {
      "type": "string",
      "default": "ena-ftp,aws-http,prefetch",
      "description": "Ordered comma-separated Kingfisher source methods."
    },
    "kingfisher_output_format": {
      "type": "string",
      "enum": ["sra", "fastq", "fastq.gz", "fasta", "fasta.gz"],
      "default": "fastq.gz",
      "description": "Preferred Kingfisher output representation."
    },
    "kingfisher_download_threads": {
      "type": ["integer", "null"],
      "minimum": 1,
      "default": null,
      "description": "Optional Kingfisher transfer-only override; defaults to --threads."
    },
    "kingfisher_check_md5": {"type": "boolean", "default": true},
    "kingfisher_force": {"type": "boolean", "default": false},
    "sracha_format": {
      "type": "string",
      "enum": ["sra", "sralite"],
      "default": "sra",
      "description": "Temporary source representation used by sracha-rs before it emits fastq.gz; sralite uses simplified quality scores."
    },
    "sracha_connections": {
      "type": ["integer", "null"],
      "minimum": 1,
      "default": null,
      "description": "Optional sracha-rs connection override; defaults to --threads."
    },
    "output_tsv": {
      "type": "boolean",
      "default": false,
      "description": "Write TSV mirrors while retaining all linked Parquet products."
    },
    "metadata_policy_version": {"type": "string", "default": "occurrence-v1"},
    "embedding_chunk_bases": {"type": "integer", "minimum": 1, "default": 8192},
    "embedding_chunk_overlap": {"type": "integer", "minimum": 0, "default": 512},
    "slurm_account": {"type": ["string", "null"]},
    "slurm_qos": {"type": ["string", "null"]},
    "slurm_partition": {"type": ["string", "null"]},
    "slurm_email": {"type": ["string", "null"]}
  },
  "oneOf": [
    {
      "required": ["manifest"],
      "properties": {
        "manifest": {"type": "string"},
        "taxid": {"type": "null"},
        "taxon_id": {"type": "null"},
        "taxon_name": {"type": "null"}
      }
    },
    {
      "required": ["taxid"],
      "properties": {
        "taxid": {"type": ["integer", "string"]},
        "manifest": {"type": "null"},
        "taxon_id": {"type": "null"},
        "taxon_name": {"type": "null"}
      }
    },
    {
      "required": ["taxon_id"],
      "properties": {
        "taxon_id": {"type": ["integer", "string"]},
        "manifest": {"type": "null"},
        "taxid": {"type": "null"},
        "taxon_name": {"type": "null"}
      }
    },
    {
      "required": ["taxon_name"],
      "properties": {
        "taxon_name": {"type": "string"},
        "manifest": {"type": "null"},
        "taxid": {"type": "null"},
        "taxon_id": {"type": "null"}
      }
    }
  ],
  "additionalProperties": true
}