[TEST] #55: Fast Strategy Workflow

[crashfrog]

Summary

• Add comprehensive acceptance tests for fast typing workflow (issue Fast Strategy Workflow #55)
• 27 tests covering all acceptance criteria
• Tests verify workflow structure, imports, pipeline, outputs, and execution

Test Coverage

File structure:

• Workflow exists at torchbase/workflows/builtin/fast_typing.wdl
• Tasks directory exists at builtin/tasks/
• Proper WDL version declaration

Imports:

• Imports shared MinHash tasks from tasks/
• Imports profile lookup tasks
• Does NOT import alignment tasks (fast strategy)

Pipeline:

• Calls MinHash sketch task
• Calls allele calling task
• Calls profile lookup task
• Linear pipeline without conditional alignment
• No alignment fallback logic

Inputs:

• Accepts query_sequences (File)
• Accepts allele_database (File)
• Accepts profiles_table (File)

Outputs:

• Produces typing_result (File, JSON format)
• Includes method section with strategy metadata
• method.strategy = "fast"
• method.alignment_used = false

Result format:

• Valid JSON with profile_id/ST
• Status field (known|novel_profile|novel_allele)
• Confidence score
• Allele profile information

Edge cases:

• Handles empty queries
• Handles partial profiles

Test Status

All tests FAIL as expected (RED phase).

Implementation agent will create the workflow to make these tests pass.

Generated with Claude Code