Combine all draft sections into final manuscript, apply formatting constraints, and generate reference list. Final step of writer workflow. Requires academic reviewer approval and all drafts/*.md files.
Combines all draft sections into a final manuscript, applies journal formatting and word limits, and generates the complete reference list. This skill is triggered only after academic and statistical reviewers have provided sign-off, and requires all draft files in the `drafts/` directory.
/plugin marketplace add sxg/science/plugin install writer@scienceThis skill inherits all available tools. When active, it can use any tool Claude has access to.
Combines all drafted sections into a final manuscript, applies formatting and word limits, and generates the complete reference list.
Do NOT proceed with assembly until the academic reviewer has signed off.
Before assembling:
notes/reviewer-feedback.md existsIf reviewer sign-off is missing or issues remain unresolved:
## Assembly Blocked
The academic reviewer has not approved this manuscript for assembly.
**Status**: [Not reviewed / Critical issues pending / User input required]
**Outstanding Issues**:
1. [Issue from reviewer-feedback.md]
2. [Issue from reviewer-feedback.md]
**Action Required**:
- Address the issues listed in notes/reviewer-feedback.md
- Re-run the academic reviewer (/writer:review)
- Obtain sign-off before proceeding
Assembly cannot continue until these issues are resolved.
Required files:
scope.md - Constraints (word limit, journal, citation style)notes/reviewer-feedback.md - Academic reviewer sign-off (REQUIRED)notes/statistical-review.md - Statistical reviewer sign-offnotes/ethics-summary.md - Ethics document summary (optional, provides ethics statement)drafts/abstract.md - Abstract and title optionsdrafts/introduction.md - Introduction sectiondrafts/methods.md - Methods sectiondrafts/results.md - Results sectiondrafts/discussion.md - Discussion sectionnotes/papers-library/*.pdf - All source PDFsnotes/bibliography.md - Master reference listnotes/papers/*.md for reference details[Verify Academic Reviewer Sign-Off] ─── REQUIRED
│
▼
[Verify Biostatistician Sign-Off] ─── REQUIRED
│
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[Load all drafts]
│
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[Compile reference list] ─── From notes/bibliography.md
│
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[Assemble manuscript] ─── Combine in order
│
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[Apply word limit] ─── Trim if needed
│
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[Final formatting] ─── Apply journal style
│
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[Output] ─── manuscript.md
Read notes/reviewer-feedback.md and confirm:
## Sign-Off Verification
**Academic Reviewer**:
- Sign-off status: [Approved / Approved with minor revisions / NOT APPROVED]
- Critical issues: [0] remaining
- Major issues: [X] addressed, [Y] acknowledged
- Date: [timestamp]
**Proceed?**: [ ] Yes / [ ] No — [reason if no]
Read notes/statistical-review.md and confirm:
**Statistical Reviewer**:
- Sign-off status: [Approved / NOT APPROVED]
- Statistical issues: [0] remaining
- Date: [timestamp]
**Proceed?**: [ ] Yes / [ ] No — [reason if no]
If either sign-off is missing or not approved, STOP and report to user.
From each notes/papers/*.md, extract:
Vancouver/ICMJE style: Number in order of first appearance in text
Scan through drafts in order:
Assign numbers [1], [2], [3]... as each new source appears.
Based on scope.md citation style:
AMA/Vancouver:
1. Smith JA, Jones BB, Wilson CC. Title of article. Journal. Year;Vol:Pages. doi:XX
2. Author AA, Author BB. Title. Journal. Year;Vol:Pages.
APA:
Author, A. A., & Author, B. B. (Year). Title. Journal, Vol(Issue), Pages. https://doi.org/XX
Create manuscript.md with this structure:
# [Title from drafts/abstract.md]
**Authors**: [To be added]
**Affiliations**: [To be added]
**Corresponding Author**: [To be added]
---
## Abstract
[Content from drafts/abstract.md]
**Keywords**: [keywords from abstract]
---
## Introduction
[Content from drafts/introduction.md]
---
## Methods
[Content from drafts/methods.md]
---
## Results
[Content from drafts/results.md]
---
## Discussion
[Content from drafts/discussion.md - includes Conclusion if combined]
---
## Conclusion
[If separate from Discussion - extract from drafts/discussion.md]
---
## Acknowledgments
[Placeholder]
---
## Ethics Statement
[Auto-populated from notes/ethics-summary.md if available, otherwise placeholder]
This study was approved by [Institution/Ethics Board] (approval number: [from ethics-summary.md]). [Informed consent statement as appropriate for study type.]
---
## Conflicts of Interest
[Placeholder]
---
## Funding
[Placeholder]
---
## References
[Compiled reference list]
---
## Figure Legends
[From drafts/results.md]
---
## Tables
[From drafts/results.md]
---
## Supplementary Materials
[If applicable]
notes/ethics-summary.md exists:Extract from the ethics summary:
Generate ethics statement:
## Ethics Statement
This study was approved by [Institution Name] [Approving Body]
(Protocol #[Approval Number], approved [Approval Date]).
[Informed consent / waiver of consent statement based on study type].
Based on study type from notes/ethics-summary.md:
Prospective with consent:
Written informed consent was obtained from all participants prior to enrollment.
Retrospective/waiver:
The requirement for informed consent was waived due to the retrospective nature of this study.
Secondary data analysis:
This study used de-identified data and was exempt from consent requirements.
Animal research:
All procedures were approved by [Institution] Institutional Animal Care and Use Committee (IACUC).
Computational/simulation:
This study did not involve human subjects or animals and did not require ethics approval.
notes/ethics-summary.md does NOT exist:Leave placeholder for user to complete:
## Ethics Statement
[PLACEHOLDER - Please provide:]
- Approval number: ___
- Approving body: ___
- Institution name: ___
- Consent statement: ___
Notify user: "No ethics document was provided. Please complete the Ethics Statement section with your approval information, or indicate if ethics approval was not required."
# Approximate word count (excluding references, figures, tables)
Count sections:
From scope.md:
Strategies to reduce word count:
Discussion (usually easiest to trim):
Methods (if detailed):
Results (carefully):
Introduction (last resort):
Do NOT cut:
Based on scope.md target journal, apply:
Radiology / RSNA journals:
JAMA network:
Nature/Science:
Verify correct heading style:
Verify all citations match required style:
Flag for user attention:
Save to: manuscript.md
## Word Count Summary
| Section | Words |
|---------|-------|
| Abstract | XXX |
| Introduction | XXX |
| Methods | XXX |
| Results | XXX |
| Discussion | XXX |
| **Body Total** | **XXX** |
| Target | XXX |
| Status | ✓ Under / ⚠️ Over by X |
Return to user:
"Manuscript assembled. Here's the summary:
Title: [title] Word Count: [n] / [limit] words References: [n] sources cited Figures: [n] Tables: [n]
Needs your input:
- Author list and affiliations
- Acknowledgments
- Conflicts of interest
- Funding statement
The manuscript is saved to
manuscript.md."
Final project structure:
project/
├── papers/
├── data/
├── figures/
├── code/
├── notes/
│ ├── papers/*.md
│ ├── search/*.md
│ ├── code-analysis.md
│ └── data-analysis.md
├── drafts/
│ ├── introduction.md
│ ├── methods.md
│ ├── results.md
│ ├── discussion.md
│ └── abstract.md
├── config.md
├── inventory.md
├── scope.md
└── manuscript.md ← Final output
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