agentsclimarketplace
Sign in

Bio workflow methods docwriter

Skill BioTender-max/awesome-bio-agent-skills/skills/omics/bio-workflow-methods-docwriter

Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.From its SKILL.md

Install
npx -y skills add BioTender-max/awesome-bio-agent-skills --skill bio-workflow-methods-docwriter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

  • no licenseNo license file was found in the repository. Code published without one is not open source by default, so using it at work is a question for whoever answers licensing questions where you are.

SKILL.md

1.6 KB, 328 tokens by cl100k_base, as published. Nobody here has run it

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

TaskAction
Evidence checklistSee reference/evidence-checklist.md
Manifest schemaschemas/run-manifest.schema.json
Validate manifestpython scripts/validate_run_manifest.py run_manifest.yaml
ExamplesSee 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

Example 1: Validate a manifest

python scripts/validate_run_manifest.py run_manifest.yaml

Troubleshooting

Issue: Missing tool versions in logs Solution: Mark as NOT CAPTURED and add a note on how to capture next time.

What ships with it: 11 files

22.0 KB alongside SKILL.md, 2 of them executable

examples/

reference/

schemas/

scripts/

templates/

Keep looking

Skills are one crate of 326,970. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.