implement-nfcore-nextflow

name	implement-nfcore-nextflow
description	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.

Implement nf-core Nextflow Skill

Use this skill only after a human has explicitly approved artifacts/1_plan.md.

Workflow

1. Confirm approval.
   • Locate artifacts/1_plan.md.
   • If approval is not explicit, stop and request approval before changing code.
2. Re-read AGENTS.md.
3. Implement only the approved scope.
4. Follow nf-core conventions:
   • use Nextflow DSL2;
   • prefer existing nf-core modules/subworkflows;
   • keep custom local modules small when needed;
   • place custom Python and R scripts in bin/;
   • use topic versions or standard versions channels where relevant;
   • assume runtime dependencies are available in the currently active Conda environment;
   • maintain nf-schema parameter validation.
5. Update coordinated files when behavior changes:
   • parameters: nextflow.config, nextflow_schema.json, docs, tests;
   • sample sheet: assets/schema_input.json, docs, tests;
   • outputs: workflow/module emits, docs/output.md, nf-test snapshots;
   • tools: module metadata, active-Conda dependency assumptions, versions, CITATIONS.md;
   • user-facing changes: README.md, CHANGELOG.md when appropriate.
6. Keep the diff small and reviewable. Do not perform unrelated template cleanup.
7. Run focused checks from the plan when feasible.
8. Save implementation notes to artifacts/2_implement.md.
9. Include:
   • approved plan reference;
   • what changed and why;
   • files changed;
   • validation attempted and results;
   • blocked checks and residual risks;
   • any follow-up work intentionally deferred.

Guardrails

• Do not commit changes.
• Do not modify generated snapshots blindly; only update snapshots when behavior is understood.
• Do not introduce new frameworks.
• Do not create, build, pull, or run containers during the current early-stage development policy.
• Do not replace nf-core scaffold patterns with custom conventions.
• If implementation reveals that the approved plan is materially wrong, stop and ask for a revised plan.