Add indel_ref_signatures to nextflow_schema.json

[Copilot]

indel_ref_signatures was introduced in nextflow.config but missing from nextflow_schema.json, causing it to be undocumented in --help output and skipped by nf-schema validation.

Changes

• nextflow_schema.json: Added indel_ref_signatures under the reference_datasets section, mirroring the structure of cosmic_ref_signatures:

  "indel_ref_signatures": {
      "type": "string",
      "format": "file-path",
      "mimetype": "text/plain",
      "description": "Path to file containing the reference indel (ID) signatures to use in SigProfilerAssignment.",
      "help_text": "You can obtain it from COSMIC website. Note that for ID signatures the GRCh37 genome version is used.",
      "fa_icon": "far fa-file-code",
      "default": "COSMIC_v3.4_ID_GRCh37.txt"
  }

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