[TEST] #16: Alignment Fallback WDL Task

[crashfrog]

Summary

Acceptance tests for alignment fallback WDL task (Issue #16).

• WDL task signature: query + allele FASTA + MinHash results → refined calls JSON
• Detects ambiguity triggers from MinHash output (low similarity, close second-best, coverage)
• Runs minimap2 alignment for flagged loci
• Refines allele calls with higher precision
• Reports novel alleles if alignment below confidence threshold
• Output JSON with status field: "confirmed" or "novel_allele"
• Containerized with minimap2
• Tests cover happy path, edge cases, and ambiguous synthetic cases

Test Status

ALL TESTS FAILING (RED PHASE) - This is expected and correct.

The alignment_fallback.wdl file does not exist yet. These tests define the contract
for the implementation agent.

27 failed tests:
- WDL file existence
- Task signature and structure
- Ambiguity detection logic
- Minimap2 integration
- Novel allele detection
- Output format validation
- Edge cases

Test plan

• Tests written following project patterns
• All tests fail with expected errors (FileNotFoundError for WDL file)
• Code style passes (flake8)
• Tests are immutable contracts for implementation

Next Steps

Implementation agent will:

1. Create alignment_fallback.wdl workflow
2. Implement ambiguity detection from MinHash results
3. Integrate minimap2 for precise alignment
4. Implement novel allele detection logic
5. Make all tests pass (GREEN phase)

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