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bio-workflow-methods-docwriter

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Generate reproducible bioinformatics/data-science Methods + run documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including a top-of-doc workflow summary, exact executed commands, tool versions, parameters, QC, and outputs.

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Source SKILL.md: https://github.com/majiayu000/claude-skill-registry/blob/HEAD/skills/data/bio-workflow-methods-docwriter/SKILL.md

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Bio Workflow Methods Docwriter

Create publication-ready Methods + internal run documentation for a specific executed bioinformatics or data science workflow run.

When to use

Use this Skill when you need to document:

  • exact workflow flow + steps that actually ran
  • tool + reference versions (and/or container image digests)
  • key parameters + QC gates
  • outputs and how to reproduce the run

Hard rules (reliability)

  • Never invent commands, tool versions, reference versions, or dataset accessions.
  • If an item is missing from evidence, write NOT CAPTURED and add a “How to capture next time” note.
  • Prefer verbatim command scripts from the workflow engine (e.g., Nextflow .command.sh) over paraphrases.
  • Keep user data private: redact tokens, credentials, and PHI.

Inputs (evidence package)

Ask for (or locate) an evidence package folder containing:

  • Workflow engine artifacts (Nextflow/Snakemake/CWL)
  • Pipeline config + params
  • Software version artifacts (e.g., nf-core software_versions.yml, conda env export, container digest)
  • Run logs + QC reports

See: reference/evidence-checklist.md

Output artifacts (always produce all 3)

  1. Workflow Summary (top of doc): 5–12 lines, plain language + step bullets.
  2. Methods & Run Documentation (METHODS.md): detailed, step-by-step.
  3. Machine-readable Run Manifest (run_manifest.yaml): exact run metadata & steps (validate).

Schema + validator:

  • Schema: schemas/run-manifest.schema.json
  • Validate: python scripts/validate_run_manifest.py run_manifest.yaml

Optional structured literature record (only if asked):

  • PaperSummary record using schemas/bio-paper-schema.yaml

Workflow

Copy this checklist into your working notes and check off as you go:

  • 1) Inventory evidence files (log what you have / what is missing)
  • 2) Build run_manifest.yaml from evidence (no guessing)
  • 3) Validate manifest (fix schema errors)
  • 4) Draft METHODS.md (summary first, then detailed steps)
  • 5) Run quality gates (versions, parameters, QC, outputs, reproducibility command)

Quality gates (must pass)

  • Every major step has: purpose • inputs • outputs • command (or NOT CAPTURED) • tool+version (or NOT CAPTURED)
  • Reproduction section includes: pinned pipeline revision • container/conda info • full run command • params/config paths
  • “Workflow Summary” appears at the very top

Quick examples (triggers)

  • “Write the Methods section for this Nextflow run directory, include exact commands and versions.”
  • “Document this Snakemake pipeline run with a workflow summary at the top and a reproducibility appendix.”
  • “Summarize this paper’s protocol into the PaperSummary schema.”