validate-hlarnaseq

name	validate-hlarnaseq
description	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.

Validate HLARNASeq Skill

Use this skill when asked to validate, review, or quality-check an implementation.

Workflow

1. Read AGENTS.md.
2. Read artifacts/1_plan.md and artifacts/2_implement.md when present.
3. Create artifacts/ if it does not exist.
4. Run .agents/skills/validate-hlarnaseq/scripts/validate.sh unless the user requests narrower validation.
   • The Nextflow testdata smoke check must run on the remote VM via ./run_tests_remote.
   • Do not replace it with local nextflow run . -profile test unless the user explicitly asks for local-only validation or remote access is blocked.
   • By default, run_tests_remote skips downloading results/ and nextflow.workdir/; set DOWNLOAD_RESULTS=1 only when output inspection is required.
5. Review changed files against the approved plan.
6. Check for nf-core pipeline risks:
   • invalid channel contracts;
   • missing emit outputs;
   • missing or inconsistent versions reporting;
   • unvalidated parameters;
   • sample sheet schema/docs drift;
   • missing docs for new outputs;
   • missing tool citations;
   • active-Conda dependency gaps;
   • tests or snapshots that do not cover new behavior.
7. Save the validation report to artifacts/3_validate.md.
8. Report findings first, ordered by severity, with file and line references.
9. If no findings are found, state that explicitly and list residual risks.

Required Report Sections

• Status summary
• Checks run
• Blocked checks
• Findings
• Plan compliance
• Residual risks
• Recommended next step

Severity Guidance

• High: likely runtime failure, incorrect scientific result, invalid schema, broken test profile, missing required active-Conda dependency.
• Medium: user-facing docs/schema drift, incomplete validation of changed workflow behavior, missing citations or versions for new tools.
• Low: maintainability issues, narrow docs gaps, minor style issues that do not affect execution.

Early-Stage Conda Policy

• Before validation, verify nf-core, nf-test, and nextflow are available from the active environment.
• If they are unavailable, try preserving the expected environment path with /bin/zsh -lc 'export PATH="/Users/gz3/apps/miniforge/envs/nf-core/bin:$PATH"; ...'.
• Do not run docker info or any containerized profile.
• Record skipped container checks as intentional policy skips, not environmental failures.
• For pipeline smoke validation, use ./run_tests_remote; it activates the remote nf-core Conda environment by default and runs pipeline_testdata_run.sh on the VM.