What is bio-workflow-methods-docwriter?

A documentation workflow that turns real Nextflow, Snakemake, or CWL run records into reproducible Methods documentation. These are workflow systems for running multi-step data analyses.

Building a run manifest, validating it, and writing a publication-ready METHODS.md file with commands, software versions, settings, provenance, and quality gates.

It bases the documentation on logs, configurations, versions, parameters, quality checks, and outputs instead of relying on memory or incomplete notes.

bio-workflow-methods-docwriter — Skill for Claude Code by fmschulz

Install

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.

Any agent

npx skills add fmschulz/omics-skills --skill bio-workflow-methods-docwriter

Clone the repo

git clone --depth 1 https://github.com/fmschulz/omics-skills

Made for: Claude Code.

Or install omics-skills, the plugin that ships this one along with the rest of its 34 skills, 4 agents.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-workflow-methods-docwriter/github.svg)](https://agentmods.dev/skills/fmschulz/omics-skills/bio-workflow-methods-docwriter)

Your own site

<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/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<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="Reviewed on agentmods" width="80" height="20"></a>

Per session 44 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,273 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector pass 7 Sept 2026

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

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	$0.01273
Opus 5.5	$0.00018	$0.00509
Sonnet 5.5	$0.00009	$0.00255
Haiku 4.5	$0.00004	$0.00127

Measured 23d ago against content hash 44a098660aae, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

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 23d ago.

The scan reads SKILL.md. This mod also ships 5 executable files (fixtures/nextflow/work/ab/cdef/.command.sh, scripts/extract_cwl_run.py, scripts/extract_nextflow_run.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

skills/bio-workflow-methods-docwriter/SKILL.md · 85 lines

How it starts

The opening of the file, as written. The whole thing — 85 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Bio Workflow Methods Docwriter

Write Methods text and run documentation from real workflow artifacts. Every command, version, and parameter comes from evidence; nothing is inferred.

Instructions

Collect the evidence package listed in reference/evidence-checklist.md: launch command, configs, engine version, tool versions or container digests, input checksums or accessions, reference and database versions, QC reports, and the final output list.
Build a draft run_manifest.yaml with the extractor for the engine:
- Nextflow: extract_nextflow_run.py reads trace.txt and the work/ task folders. --tool-versions is a JSON mapping of process name to {"tool": ..., "version": ...}; --outputs-manifest lists one final output path per line.
- Snakemake: extract_snakemake_run.py reads a JSONL file with one record per job (rule, status, tool, version, command, inputs, outputs). Assemble it from --printshellcmds logs and the version records; see fixtures/snakemake/jobs.jsonl.
- CWL: extract_cwl_run.py reads one normalized JSON record (run metadata plus steps and outputs), not a raw CWLProv folder; see fixtures/cwl/provenance.json.
Fill the remaining fields from evidence only. While drafting, mark a missing value NOT CAPTURED; the final manifest must not contain it. If the value cannot be recovered, record the gap under limitations and do not call the manifest reproducible.
Validate the manifest against schemas/run-manifest.schema.json with validate_run_manifest.py.
Draft METHODS.md from templates/methods_report.md: workflow summary at the top, then inputs, exact rerun command, environment, steps as executed, QC, outputs, and limitations.
For manuscript Methods prose, hand the manifest to /scientific-writing. Keep script names, internal flags, and runtime bookkeeping in Methods or the supplement, not in Results.

Read the full file on GitHub · 85 lines

Files

What ships with it

21 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.

Changes

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.

23d ago Changed · +11 lines 44a098660aae
1mo ago First seen · 74 lines · 44 tokens per session scan A 955e201f61a1

Subscribe to this mod's changes

bio-workflow-methods-docwriter is a skill published in the GitHub repository fmschulz/omics-skills (11 stars, last pushed 23d ago), licensed MIT. It adds 44 tokens to every session and 1,273 once invoked, about $0.0002 per session on Opus 5.5. 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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