Conduct scoping conversation with user to define research question, key findings, and constraints. Generates scope.md that guides all subsequent steps. Second step of writer workflow. Requires inventory.md to exist.
Conducts a focused conversation to establish the research scope, then generates a scope document that guides all subsequent writing.
inventory.md must exist (from context-ingestion step)notes/ethics-summary.md may exist (if ethics document was provided)[Read inventory.md and notes/ethics-summary.md]
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[Ask: Research Question]
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[Ask: Key Findings] ─── Cross-reference with data inventory
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[Confirm: Constraints] ─── From config.md
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[Ask: Additional Context]
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[Ethics Scope Comparison] ─── If ethics docs exist, compare and confirm discrepancies
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[Generate scope.md and notes/ethics-scope-comparison.md]
Before asking questions, read to understand:
inventory.mdAlso check if notes/ethics-summary.md exists. If it does, read it to understand:
This context helps ask informed questions and validate user responses. Note that ethics approval scope is often broader than actual research scope.
Ask questions one at a time. Wait for response before proceeding.
"What research question does this study address?
Try to frame it as a specific, answerable question. For example:
- 'Does the proposed method outperform existing approaches on benchmark datasets?'
- 'What factors predict the observed outcome in this population?'"
Good research questions have:
If vague, ask follow-up to clarify.
"What are the key findings from your analysis?
I can see from your data that you have [summarize data files from inventory]. What were the main results?"
Cross-check with inventory:
figures/Ask for:
"I see from your config that you're targeting [journal] with a [word_limit] word limit.
Are there any other constraints I should know about?
- Specific formatting requirements?
- Required sections or subsections?
- Exclusions (topics to avoid)?"
"Is there anything else I should know about this study?
For example:
- Study limitations you want to acknowledge
- Specific papers you want to cite or respond to
- Practical implications to emphasize"
Skip this step if notes/ethics-summary.md does not exist.
After gathering user's stated scope, compare it against the ethics document and present discrepancies for confirmation.
Present to user:
"I've compared your stated research scope with the ethics/governance document.
Aspect Ethics Document Your Stated Scope Population [from ethics] [from user] Sample size [from ethics] [from user] Endpoints [from ethics] [from user] Procedures [from ethics] [from user] Please confirm:
- Are these differences intentional? (subset of approved protocol)
- Any context for the narrower scope? (e.g., 'subset of data analyzed')
- Anything I've misunderstood?"
Create notes/ethics-scope-comparison.md:
# Ethics vs Actual Scope Comparison
**Generated**: [timestamp]
**Ethics Source**: [filename from ethics-summary.md]
## Comparison
| Aspect | Ethics Document | Actual Scope | Explanation |
|--------|-----------------|--------------|-------------|
| Population | [from ethics] | [from user] | [user explanation] |
| Sample size | [from ethics] | [from user] | [user explanation] |
| Endpoints | [from ethics] | [from user] | [user explanation] |
| Procedures | [from ethics] | [from user] | [user explanation] |
## User Confirmation
- **Differences intentional?**: [yes/no + explanation]
- **Context for narrower scope**: [user response]
- **Clarifications**: [any corrections to understanding]
## Implications for Manuscript
- [Note any elements from ethics doc that should NOT appear in manuscript]
- [Note any elements that need careful framing]
This document provides audit trail and guides later steps when they need to understand why ethics approval scope and manuscript scope differ.
After conversation, generate structured scope document:
# Manuscript Scope
Generated: [timestamp]
## Research Question
[User's research question, cleaned up if needed]
## Hypothesis
[Inferred or stated hypothesis]
## Key Findings
### Primary Finding
[Main result with expected statistics]
### Secondary Findings
1. [Finding 2]
2. [Finding 3]
### Negative/Null Results
- [If any]
## Target Publication
- **Journal**: [from config]
- **Word Limit**: [from config]
- **Citation Style**: [from config]
## Constraints
- [Any additional constraints from conversation]
## Study Context
### Population
[Inferred from data/conversation]
### Methods Overview
[Brief summary based on code inventory]
### Limitations to Address
- [User-specified limitations]
## Materials Available
### Literature
- [n] PDFs in papers/ folder
- Key papers to emphasize: [if mentioned]
### Data
- [List key data files and what they contain]
### Figures
- [List figures and what they show]
### Code
- Repository: [url]
- Analysis approach: [inferred from code inventory]
### Ethics Documents
- **Available**: [yes/no]
- **Ethics Approval Number**: [from ethics-summary.md or "to be added manually"]
- **Scope Notes**: [see notes/ethics-scope-comparison.md for differences]
## Writing Guidance
### Tone
[Infer from journal: clinical, technical, etc.]
### Emphasis
[What to highlight based on conversation]
### Avoid
[What to minimize or exclude]
Before saving scope.md, verify:
Save to:
project/scope.md - Main scope documentnotes/ethics-scope-comparison.md - Ethics comparison (if ethics docs exist)Summarize back to user:
"I've created the scope document. Here's the summary:
Research Question: [question] Primary Finding: [finding]
Target: [journal], [word_limit] wordsReady to proceed with literature review?"
Return to parent skill.