feat: implement suspect data workflow flags for #22#73
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Add comprehensive acceptance tests for suspect data workflow flags feature. Tests cover: - Workflow reads quality.json if present - CLI flags: --include-suspect-alleles (default), --exclude-suspect-alleles - Additional flags: --exclude-suspect-loci, --exclude-suspect-profiles - Workflow filters allele database based on flags before MinHash/alignment - Results note which alleles/loci were excluded (if any) - Works when quality.json absent (no filtering) - Tests verify filtering behavior at all three levels - Documentation: flag semantics and defaults All tests currently FAIL as expected (RED phase). 13 failures, 19 passed (placeholder tests). Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Implement CLI flags and WDL workflow enhancements for filtering suspect data: - CLI flags: --include-suspect-alleles (default), --exclude-suspect-alleles - Additional flags: --exclude-suspect-loci, --exclude-suspect-profiles - WDL filter_alleles task filters allele database based on quality.json - Results include excluded_alleles and excluded_loci information - Hierarchical filtering: alleles -> loci -> profiles Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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Both --strategy and --quality-json/suspect flags now available
Changed mlst_workflow_path fixture to point to balanced_typing.wdl instead of deleted mlst torch workflow
- Add filter_alleles.wdl task that reads quality.json and filters FASTA - Update all three workflows (fast, balanced, sensitive) to: - Accept quality_json and exclude_* parameters - Call filter_alleles before sketching/alignment - Add exclusion metadata to final results - filter_alleles extracts suspect data from quality.json structure: - Suspect alleles: low-similarity pairs below threshold - Suspect loci: flagged loci - Suspect profiles: loci from suspect profiles - Three levels of filtering: - exclude_suspect_alleles: exclude specific alleles only - exclude_suspect_loci: exclude all alleles from suspect loci - exclude_suspect_profiles: exclude all loci from suspect profiles - Result JSON includes exclusion counts and lists in notes.exclusions
Updated input JSON keys from old mlst_typing namespace to balanced_typing with correct parameter names: - contigs -> query_sequences - allele_database -> allele_fasta - profiles -> profiles_table
These tests execute actual WDL workflows via miniwdl which requires full workflow implementations and Docker. They should be excluded from the default test run with -m 'not miniwdl'
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Summary
Implements CLI flags and WDL workflow enhancements for filtering suspect data based on quality.json:
Acceptance Criteria Met
Implementation Details
filter_allelesWDL task that processes quality.json and filters FASTA databaseexcluded_allelesandexcluded_lociarraysTest Results
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