sop-writer

name sop-writer description Write GCP-compliant standard operating procedures for laboratory, clinical, or research workflows; use when a reproducible SOP with roles, steps, and control points is required. license MIT author AIPOCH Source : https://github.com/aipoch/medical-research-skills SOP Writer Generate compliant Standard Operating Procedures. Quick Check Use this command to verify that the packaged script entry point can be parsed before deeper execution. python -m py_compile scripts/main.py Audit-Ready Commands Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths. python -m py_compile scripts/main.py python scripts/main.py -- help When to Use Use this skill when the task is to Write GCP-compliant Standard Operating Procedures for labs and clinical. Use this skill for protocol design tasks that require explicit assumptions, bounded scope, and a reproducible output format. Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence. Workflow Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions. Use the packaged script path or the documented reasoning path with only the inputs that are actually available. Return a structured result that separates assumptions, deliverables, risks, and unresolved items. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion. Use Cases Sample processing SOPs Equipment calibration SOPs Safety procedure documentation GCP compliance procedures Parameters procedure_name : SOP title scope : Applicable areas responsibility : Who performs Returns ISO 15189 compliant SOP Version control section Signature page template Example Input: Blood sample processing Output: Complete SOP with materials, methods, QC checks References references/audit-reference.md - Supported SOP scope, audit commands, and fallback boundaries Risk Assessment Risk Indicator Assessment Level Code Execution Python/R scripts executed locally Medium Network Access No external API calls Low File System Access Read input files, write output files Medium Instruction Tampering Standard prompt guidelines Low Data Exposure Output files saved to workspace Low Security Checklist No hardcoded credentials or API keys No unauthorized file system access (../) Output does not expose sensitive information Prompt injection protections in place Input file paths validated (no ../ traversal) Output directory restricted to workspace Script execution in sandboxed environment Error messages sanitized (no stack traces exposed) Dependencies audited Prerequisites No additional Python packages required. Evaluation Criteria Success Metrics Successfully executes main functionality Output meets quality standards Handles edge cases gracefully Performance is acceptable Test Cases Basic Functionality : Standard input → Expected output Edge Case : Invalid input → Graceful error handling Performance : Large dataset → Acceptable processing time Lifecycle Status Current Stage : Draft Next Review Date : 2026-03-06 Known Issues : None Planned Improvements : Performance optimization Additional feature support Output Requirements Every final response should make these items explicit when they are relevant: Objective or requested deliverable Inputs used and assumptions introduced Workflow or decision path Core result, recommendation, or artifact Constraints, risks, caveats, or validation needs Unresolved items and next-step checks Error Handling If required inputs are missing, state exactly which fields are missing and request only the minimum additional information. If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment. If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback. Do not fabricate files, citations, data, search results, or execution outcomes. Input Validation This skill accepts requests that match the documented purpose of sop-writer and include enough context to complete the workflow safely. Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond: sop-writer only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill. Response Template Use the following fixed structure for non-trivial requests: Objective Inputs Received Assumptions Workflow Deliverable Risks and Limits Next Checks If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness. When Not to Use Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first. Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences. Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope. Required Inputs Field Required Format/Source Example If Missing User task description Yes Text Research question, writing goal, analysis objective Stop and ask user to provide Primary input material Depends on task Text, file path, ID, table, or literature PMID, PDF, CSV, DOCX, keywords, etc. Specify which material type is missing Output preference No Text Language, format, target journal, template Use skill default format Output Contract Primary output: Structured result or target file aligned with this skill's objective. Optional output: Intermediate check notes, issue list, supplementary suggestions, or generated file paths. Format requirement: Unless the user specifies otherwise, prefer stable, reviewable Markdown or JSON; if the skill's bundled script requires a fixed format, use that format. If partially complete: Must explicitly mark as PARTIAL and state which steps are completed and which remain. Failure Handling Missing critical input: Explicitly state which fields, files, or identifiers are missing and pause. Script, template, or resource execution failure: Report the failing step, likely cause, and recovery suggestions — do not silently degrade. Partial completion only: Return the verified portion first, then list remaining blockers and suggested next steps. User Checkpoints Before executing batch processing, overwriting files, long-running searches, or multi-stage generation, confirm scope and output format with the user. Before proceeding when a key judgment is ambiguous, evidence is insufficient, or the workflow is entering the next stage, confirm with the user. Quick Validation Check that key scripts, templates, or reference file paths this skill depends on exist. Check that the final output contains the core fields, sections, or files specified for this task. Check that results clearly mark assumptions, limitations, and incomplete items.