helix-cli simulate config schema (v1)

Top-level fields

• session_id (optional): string label for the session; defaults to cli_session.
• project_id (optional): propagated into run metadata.
• author (optional): propagated into run metadata.
• runs (required): list of run specs.

Per run (common)

• run_id (optional): defaults to guide_id if omitted.
• guide_id (required): identifier for the guide/peg.
• edit_type (required): crispr or prime.
• sequence (required): template sequence string.
• target_locus (optional): human-readable locus label.
• pam_index / cut_index (optional): integers; used by some visualizers/engines.
• pam_profile (optional): defaults to SpRY_NNN (permissive) in CLI simulate.
• metadata (optional): arbitrary dict; propagated to reports and UI chips.

CRISPR-specific

• No extra fields beyond the common set (future parameters may be added).

Prime-specific (edit_type: prime)

• prime.pbs_sequence (required): PBS sequence.
• prime.rt_sequence (required): RTT sequence.
• prime.nick_guide_id (optional): label for the nicking guide.
• prime.nick_cut_index (optional): nick position index.
• prime.spacer (optional): peg spacer; defaults to guide_id.
• prime.pam_profile (optional): PAM profile name (default SpRY_NNN).
• prime.draws (optional): integer draws for stochastic sampling.
• prime.seed (optional): RNG seed for reproducibility.

Example: CRISPR

{
  "session_id": "batch_crispr_demo",
  "project_id": "P1234",
  "runs": [
    {
      "run_id": "demo_crispr_g2",
      "guide_id": "g2",
      "edit_type": "crispr",
      "sequence": "ACGT...",
      "target_locus": "BRCA1 exon 11",
      "pam_index": 123,
      "cut_index": 126,
      "metadata": {"sample_id": "S1"}
    }
  ]
}

Example: Prime

{
  "session_id": "batch_prime_demo",
  "runs": [
    {
      "run_id": "demo_prime_g3",
      "guide_id": "g3",
      "edit_type": "prime",
      "sequence": "TGCA...",
      "target_locus": "PCSK9 exon 1",
      "pam_index": 88,
      "cut_index": 91,
      "prime": {
        "pbs_sequence": "ACTG",
        "rt_sequence": "GATTACA",
        "nick_guide_id": "g3n",
        "nick_cut_index": 104,
        "pam_profile": "SpRY_NNN",
        "draws": 10000,
        "seed": 42
      },
      "metadata": {"sample_id": "S2"}
    }
  ]
}