[Epic 6] Documentation & Polish

[smagala]

Description

Complete documentation and finalize code quality.

Stories

• 6.1 Write usage documentation (45 min)
• 6.2 Write output documentation (45 min)
• 6.3 Create nextflow_schema.json (30 min)
• 6.4 Update CITATIONS.md (20 min)
• 6.5 Add MultiQC integration (45 min)
• 6.6 Run nf-core lint (30 min)
• 6.7 Create CHANGELOG.md (15 min)

Acceptance Criteria

• docs/usage.md documents all parameters with examples
• docs/output.md describes all output files
• nextflow_schema.json enables nf-core launch
• CITATIONS.md includes all tool citations (bwa, samtools, ivar, etc.)
• MultiQC custom content displays denver-specific results
• nf-core lint passes with no warnings
• CHANGELOG.md documents v1.0.0 features

Estimated LoE

3.75 hours

Dependencies

Epics 1-5 complete

[smagala]

Completed in PR #54

Deliverables

• usage.md: Complete rewrite with DENV-specific content (samplesheet format, reference structure, parameters, troubleshooting)
• output.md: Expanded to document all 9 output directories
• CITATIONS.md: Added 6 missing tool citations (BWA, bedtools, iVar, MAFFT, Nextclade, SAMtools)
• CHANGELOG.md: Comprehensive v1.0.0 release notes

Stories Completed

• 6.1 Usage documentation ✓
• 6.2 Output documentation ✓
• 6.3 nextflow_schema.json (already existed) ✓
• 6.4 CITATIONS.md ✓
• 6.5 MultiQC (already integrated) ✓
• 6.6 nf-core lint (passes with 1 accepted failure) ✓
• 6.7 CHANGELOG.md ✓

Estimate vs Actual

• Estimated: 3.75 hours
• Actual: ~30 minutes (much already completed in prior work)

Notes

• nextflow_schema.json and MultiQC integration were completed during earlier epics
• The 1 lint failure is the accepted SnakeYAML compatibility fix