Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add fmschulz/omics-skills --skill bio-workflow-methods-docwritergit clone --depth 1 https://github.com/fmschulz/omics-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/fmschulz/omics-skills/bio-workflow-methods-docwriter)<a href="https://agentmods.dev/skills/fmschulz/omics-skills/bio-workflow-methods-docwriter"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-workflow-methods-docwriter.svg" alt="Measured on agentmods" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00044 | $0.00777 |
| Opus 5 | $0.00022 | $0.00388 |
| Sonnet 5 | $0.00009 | $0.00155 |
| Haiku 4.5 | $0.00004 | $0.00078 |
Grade A, and why
bio-workflow-methods-docwriter scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 74 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Bio Workflow Methods Docwriter
Create publication-ready Methods and run documentation from real workflow artifacts.
Instructions
- Collect the workflow evidence package (logs, configs, version files).
- Build
run_manifest.yamlstrictly from evidence. - Validate the manifest against the schema.
- Draft
METHODS.mdwith a concise workflow summary at the top. - Verify QC gates and reproducibility details are captured.
Resolve the installed skill with:
METHODS_SKILL="${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
What ships with it
22 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- examples/run_manifest.example.yaml 1.6 KB
- fixtures/cwl/provenance.json 510 B
- fixtures/nextflow/outputs.txt 21 B
- fixtures/nextflow/tool-versions.json 52 B
- fixtures/nextflow/trace.txt 135 B
- fixtures/nextflow/work/ab/cdef/.command.in 12 B
- fixtures/nextflow/work/ab/cdef/.command.out 21 B
- fixtures/nextflow/work/ab/cdef/.command.sh 31 B runs code
- fixtures/snakemake/jobs.jsonl 177 B
- fixtures/snakemake/outputs.txt 21 B
- reference/evidence-checklist.md 2.0 KB
- reference/standards.md 719 B
- requirements.txt 18 B
- schemas/bio-paper-schema.yaml 2.6 KB
- schemas/run-manifest.schema.json 5.3 KB
- schemas/workflow-run-schema.yaml 2.7 KB
- scripts/extract_cwl_run.py 1.7 KB runs code
- scripts/extract_nextflow_run.py 6.7 KB runs code
- scripts/extract_snakemake_run.py 2.3 KB runs code
- scripts/validate_run_manifest.py 2.9 KB runs code
- templates/methods_report.md 1.0 KB
- templates/paper_summary.yaml 627 B
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 7d ago First seen · 74 lines · 44 tokens per session scan A 955e201f61a1
bio-workflow-methods-docwriter is a skill published in the GitHub repository fmschulz/omics-skills (7 stars, last pushed 2d ago), licensed MIT. It adds 44 tokens to every session and 777 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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