Bioinformatics Workflow Code Review Roadmap

Role: Senior Bioinformatician and Computational Biology Platform Architect.

Context

• Orchestration system: {{workflow_engine}}
• Primary assay type: {{sequencing_data_type}}
• Infrastructure backend: {{cloud_compute_environment}}
• Container repository: {{container_registry_source}}
• Determinism benchmark: {{reproducibility_standard}}
• Peak resource limit: {{memory_allocation_ceiling}}

Task

Draft an operational code review plan to inspect genomic workflow definitions, task directives, container dependencies, and reference asset management for computational integrity.

Method

1. Audit workflow source files in {{workflow_engine}} for pinned process versions, fixed random seeds, and immutable reference dependencies.
2. Validate that container references resolve strictly to {{container_registry_source}} using immutable SHA256 digests.
3. Inspect memory and CPU resource directives per task to ensure jobs remain below {{memory_allocation_ceiling}}.
4. Verify intermediate artifact caching, staging, and cleanup routines across {{cloud_compute_environment}}.
5. Examine task scripts processing {{sequencing_data_type}} for silent error propagation and unhandled pipe failures.
6. Cross-reference alignment and variant calling parameter changes against {{reproducibility_standard}}.
7. Prepare an engineer-ready review workflow with assigned verification stages and triage criteria.

Constraints

• MUST require container image digests rather than mutable image tags (e.g., :latest).
• MUST NOT permit task configurations that fail silently on non-zero exit codes in shell pipelines.
• Review stages must account for compute cost constraints in {{cloud_compute_environment}}.
• Keep recommendations tightly focused on workflow code structure and reproducibility.

Output format

Generate a markdown plan formatted as:

• Review Overview (2-3 sentences defining the pipeline milestone)
• Workflow Integrity Checklist (table with Category, File Pattern, Inspection Rule, and Blocking Level)
• Compute & Container Audit Steps (4-5 chronological evaluation steps)
• Acceptance Protocol (bulleted criteria required to approve the pull request)

Self-review

• Confirm that the instructions specifically address {{workflow_engine}} syntax patterns.
• Validate that memory limits from {{memory_allocation_ceiling}} are explicitly evaluated in the plan.
• Ensure all output sections are complete without placeholder text.