Bio Workflow Methods Docwriter

Create publication-ready Methods and run documentation from real workflow artifacts.

Instructions

Collect the workflow evidence package (logs, configs, version files).
Build run_manifest.yaml strictly from evidence.
Validate the manifest against the schema.
Draft METHODS.md with a concise workflow summary at the top.
Verify QC gates and reproducibility details are captured.

Resolve the installed skill with:

METHODS_SKILL="${METHODS_SKILL:-$HOME/.agents/skills/bio-workflow-methods-docwriter}"

Quick Reference

| Task | Action | |------|--------| | Evidence checklist | See reference/evidence-checklist.md | | Standards to align with | See reference/standards.md | | Manifest schema | schemas/run-manifest.schema.json (LinkML source: schemas/workflow-run-schema.yaml) | | Drafting templates | METHODS.md template, paper-summary YAML | | Extract a Nextflow draft | uv run "$METHODS_SKILL/scripts/extract_nextflow_run.py" --help | | Extract Snakemake evidence | uv run --script "$METHODS_SKILL/scripts/extract_snakemake_run.py" --help | | Extract CWL evidence | uv run --script "$METHODS_SKILL/scripts/extract_cwl_run.py" --help | | Validate manifest | uv run "$METHODS_SKILL/scripts/validate_run_manifest.py" run_manifest.yaml | | Examples | See examples/ |

Input Requirements

Workflow artifacts (Nextflow/Snakemake/CWL logs and configs)
Tool version records or container digests
QC reports and output manifests

Output

METHODS.md (agent-authored; workflow summary + detailed steps)
run_manifest.yaml (machine-readable run manifest)
Artifact contract: schemas/run-manifest.schema.json
LinkML source: schemas/workflow-run-schema.yaml
Paper-summary schema: schemas/bio-paper-schema.yaml

Quality Gates

[ ] No invented commands, versions, or parameters
[ ] Every step has inputs, outputs, and versions captured
[ ] Commands were sourced from task scripts, not environment-bearing wrappers, and contain no credentials
[ ] No NOT CAPTURED, UNKNOWN, or TBD placeholder remains in a required field
[ ] Workflow summary appears at top of METHODS.md
[ ] The engine-specific extractor output passes validate_run_manifest.py; the fixture-backed Nextflow path proves trace, task script, input, output, version, and final-output evidence end to end.

Examples

Example 1: Validate a manifest

METHODS_SKILL="${METHODS_SKILL:-$HOME/.agents/skills/bio-workflow-methods-docwriter}"
uv run "$METHODS_SKILL/scripts/validate_run_manifest.py" run_manifest.yaml

Troubleshooting

Issue: Missing tool versions in logs Solution: Use NOT CAPTURED only while assembling a draft. The final validator rejects it; recover the version from provenance or report the missing evidence in limitations without claiming a reproducible manifest.