wtsi-hgi

Orchestrates standalone or caller-batched bug fixes via implementor and reviewer subagents using TDD. Handles bugs and verified review findings sequentially, tracks them in a dated checklist, and commits each fix without disrupting a surrounding PR-resolution batch.

Resolve GitHub PR review comments from humans and Copilot, including reviews already auto-requested or in progress. Use for verified comment resolution, sequential bugfix batching, one-push CI/Copilot cycles, and SHA-aware waits that avoid stale-event loops.

Shared conventions for Go projects. Copyright boilerplate, code quality, GoConvey testing, architecture, and commands. Referenced by go-implementor, go-reviewer, and workflow skills.

Go TDD implementation workflow. References implementation-principles, go-conventions, testing-principles, and agent-conduct.

Review Go implementations against spec acceptance tests. References implementation-principles, go-conventions, testing-principles, and agent-conduct.

Shared cross-language delivery workflow and guidance for implementing the simplest sufficient solution, maximizing reuse of existing code, and avoiding speculative abstractions, dependencies, and refactors. Use when implementing or reviewing code in any language.

Nextflow DSL 2 TDD implementation workflow. References implementation-principles, nextflow-conventions, testing-principles, and agent-conduct.

Review Nextflow DSL 2 implementations against spec acceptance tests. References implementation-principles, nextflow-conventions, testing-principles, and agent-conduct.

Implement an approved scoped change in WxS-QC, preserving Python/Hail pipeline contracts, numbered stage behavior, config compatibility, and strict scope discipline.

Validate WxS-QC changes by running integration smoke tests, reviewing pipeline contracts, checking scope discipline, and documenting blocked integration/Hail/Spark validation.

Create a small, reviewable implementation plan for WxS-QC, an old Python/Hail QC pipeline with limited tests, using references/plan-template.md, scoped files, acceptance criteria, and validation steps. Ends by requesting human approval before implementation.

Validate nf-core/hlarnaseq changes by running available nf-core, nf-test, remote Nextflow testdata via run_tests_remote, and pre-commit checks; review plan compliance; and write artifacts/3_validate.md with findings and residual risks.

Implement an approved one-iteration plan for nf-core/hlarnaseq using Nextflow DSL2, Python, or R as appropriate. Preserves nf-core conventions, updates coordinated schema/docs/tests, and writes artifacts/2_implement.md.

Create a small, reviewable one-iteration plan for nf-core/hlarnaseq. Use for features, fixes, refactors, module additions, parameter changes, docs updates, or test work. Saves artifacts/1_plan.md and stops for human approval.