bio-workflow-methods-docwriter
Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-workflow-methods-docwriter --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Bio Workflow Methods Docwriter Create publication-ready Methods and run documentation from real workflow artifacts. ## Instructions 1. Collect the workflow evidence package (logs, configs, version files). 2. Build `run_manifest.yaml` strictly from evidence. 3. Validate the manifest against the schema. 4. Draft `METHODS.md` with a concise workflow summary at the top. 5. Verify QC gates and reproducibility details are captured. ## Quick Reference | Task | Action | |------|--------| | Evidence checklist | See `reference/evidence-checklist.md` | | Manifest schema | `schemas/run-manifest.schema.json` | | Validate manifest | `python 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` (workflow summary + detailed steps) - `run_manifest.yaml` (machine-readable run manifest) ## Quality Gates - [ ] No invented commands, versions, or parameters - [ ] Every step has inputs, outputs, and versions captured - [ ] Workflow summary appears at top of `METHODS.md` ## Examples ### E
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Validate a manifest
- Troubleshooting
python scripts/validate_run_manifest.py run_manifest.yaml
What does the bio-workflow-methods-docwriter skill do?
Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-workflow-methods-docwriter --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.