name: bio-workflow-methods-docwriter description: 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.

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.”