plan-pipeline-change

name	plan-pipeline-change
description	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.

Plan Pipeline Change Skill

Use this skill when the user asks to plan any change to nf-core/hlarnaseq, or when implementation is requested but no approved plan exists.

Workflow

1. Read the user request and restate the target behavior.
2. Read AGENTS.md and enforce repository constraints.
3. Inspect the relevant pipeline files before planning. Common files include:
   • main.nf
   • workflows/hlarnaseq.nf
   • nextflow.config
   • nextflow_schema.json
   • assets/schema_input.json
   • conf/test.config
   • tests/default.nf.test
   • modules.json
   • docs/usage.md
   • docs/output.md
4. Check whether an existing nf-core module or subworkflow should be used before proposing custom process code.
5. If you need to clarify anything, ask questions.
6. Produce a minimal one-iteration plan using references/plan-template.md.
7. Save the complete proposed plan to artifacts/1_plan.md.
8. Keep scope tight:
   • list in-scope and out-of-scope items;
   • avoid broad rewrites unless explicitly requested;
   • keep the expected review under about 30 minutes.
9. Include coordinated file updates for any changed behavior:
   • parameters: nextflow.config, nextflow_schema.json, docs, tests;
   • sample sheet columns: assets/schema_input.json, docs, tests;
   • outputs: module/workflow emits, docs/output.md, nf-test snapshots;
   • tools: module metadata, active-Conda dependency assumptions, CITATIONS.md, versions.
10. Include validation commands with pass criteria and note likely blockers.
11. Stop and request human approval. Do not implement.

Early-Stage Conda Policy

• Treat runtime tools as provided by the currently active Conda environment.
• Plan custom Python and R scripts under bin/.
• Do not plan container creation, packaging, pulls, or containerized execution profiles.
• When adding a tool, document the Conda environment expectation, versions reporting, and citation impact instead of adding container packaging.

Output

Return the completed plan sections in the same order as references/plan-template.md.

At the end, add:

Approval needed: Please confirm this plan is approved. I will not implement until you approve.

Persist the same content to artifacts/1_plan.md before finishing.