bio-workflow-methods-docwriter

Generate METHODS.md and run_manifest.yaml from Nextflow, Snakemake, and CWL workflow artifacts.

7|1|Updated Feb 2, 2026

Search Tags:#workflow #documentation #methods #generate #reproducibility #nextflow #snakemake

Ready to run

npx skills add https://github.com/fmschulz/omics-skills --skill bio-workflow-methods-docwriter

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bio-workflow-methods-docwriter
Source: https://github.com/fmschulz/omics-skills/tree/main/skills/bio-workflow-methods-docwriter
Command: npx skills add https://github.com/fmschulz/omics-skills --skill bio-workflow-methods-docwriter

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pyyaml, jsonschema, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Researchers often lack a reproducible record of how workflow runs were performed, making publication and auditability difficult.

Core Features & Use Cases

Generate publication-ready Methods and run documentation directly from workflow artifacts (Nextflow, Snakemake, CWL).
Build a machine-readable run_manifest.yaml capturing commands, tool versions, parameters, QC gates, and outputs.
Produce a concise workflow summary in METHODS.md suitable for methods sections of manuscripts.

Quick Start

Collect the workflow evidence package and run the extractor to produce METHODS.md and run_manifest.yaml.

Frequently Asked Questions about bio-workflow-methods-docwriter

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I generate reproducible Methods documentation from Nextflow or Snakemake workflow run artifacts?▼

To generate reproducible Methods documentation from Nextflow or Snakemake workflows, collect run logs, configs, and tool versions, then run the extractor to produce a publication-ready METHODS.md and a machine-readable run_manifest.yaml.

What is a run_manifest.yaml and how does it capture workflow reproducibility?▼

A run_manifest.yaml is a machine-readable file capturing exact commands, tool versions, parameters, QC gates, and outputs from workflow run artifacts. It enforces manifest validation against the run-manifest schema to ensure full reproducibility.

Can I use this to create publication-ready methods sections from CWL workflows?▼

Yes, you can create publication-ready methods sections from CWL workflows. The extractor applies to Nextflow, Snakemake, and CWL, collecting logs and configs to generate a concise workflow summary in METHODS.md suitable for manuscripts.

What's the best way to capture tool versions and parameters from a workflow run?▼

The best way to capture tool versions and parameters is to collect the workflow evidence package and run the extractor. It automatically parses workflow artifacts to document exact commands, versions, parameters, QC gates, and outputs into run_manifest.yaml.

Do I need pyyaml and jsonschema to validate the workflow run manifest?▼

Yes, you need pyyaml and jsonschema as dependencies to validate the workflow run manifest. The Skill enforces manifest validation against the run-manifest schema to guarantee that captured commands, versions, and outputs maintain reproducibility.