CLI Strategy Routing

[crashfrog]

Parent

Part of generalized allelic typing system design (discussed in conversation 2026-05-22)

What to build

Add --strategy [fast|balanced|sensitive] flag to torchbase run command. CLI routes to appropriate built-in workflow based on strategy selection. Default is "balanced".

Error handling: If torch has embedded workflow (main.wdl) and user specifies --strategy, raise error: "Cannot use --strategy with torch-embedded workflows".

Routing logic:

• No torch workflow + --strategy fast → builtin/fast_typing.wdl
• No torch workflow + --strategy balanced → builtin/balanced_typing.wdl
• No torch workflow + --strategy sensitive → builtin/sensitive_typing.wdl
• Torch has workflow + --strategy specified → ERROR
• Torch has workflow + no --strategy → use torch workflow

Integrates with multi-scheme support from #53 to pass concatenated files to workflows.

Acceptance criteria

• --strategy flag added to CLI with choices [fast, balanced, sensitive]
• Default strategy is "balanced"
• CLI routes to correct built-in workflow file based on strategy
• Error raised if strategy used with torch-embedded workflow
• Multi-scheme concatenation (from Multi-Scheme Torch Support #53) integrated
• Help text explains strategy options and restrictions
• Tests verify routing logic and error conditions

Blocked by

#53 - Multi-Scheme Torch Support
#55 - Fast Strategy Workflow
#56 - Balanced Strategy Workflow
#57 - Sensitive Strategy Workflow

[crashfrog]

Already resolved by #78