[Epic] Pipeline Bugfixes - Pre-Release Stabilization

[smagala]

Overview

Tracking epic for bug fixes required before tagging a stable release of the Denver (DENV) pipeline.

Scope

• Critical bugs that prevent correct pipeline execution
• Channel/workflow logic issues
• Container compatibility fixes
• Output correctness issues

Exit Criteria

• All child issues resolved
• Pipeline completes full test dataset (8 samples × 6 serotypes)
• Serotype calls match expected values
• No container/dependency issues
• Ready for v1.0.0 release tag

Related

• Testing Epic: [Epic] Pipeline Testing and Validation #55
• Initial Test Run: [Run 56] Initial pipeline validation - PRJNA973096 full dataset #56