review
Review and critique a scientific manuscript, identifying critical issues with detailed explanations and recommendations. Produces a structured review with accept/revise/reject recommendation.
assembler
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.
code-analyzer
Analyze GitHub repository to extract methodology and generate the Methods section. Fourth step of writer workflow. Requires scope.md and cloned code/ repository.
context-ingestion
Scan project folder structure, validate organization, clone GitHub repository, and generate an inventory of available materials. First step of writer workflow. Use when starting a new manuscript project.
literature-review
Process user-provided PDFs using isolated subagents, generate structured notes, synthesize findings, and draft the Introduction section. Third step of writer workflow. Requires scope.md.
writer
Draft scientific research manuscripts from research data. Use when user wants to write a research paper, has a project folder with papers, data, figures, and a GitHub repository link. Orchestrates context-ingestion, scoping, literature-review, code-analyzer, results-interpreter, synthesis, and assembler sub-skills.
results-interpreter
Analyze CSV data files and interpret figures to generate the Results section. Fifth step of writer workflow. Requires scope.md, data/ folder with CSVs, and figures/ folder with images.
scoping
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.
synthesis
Synthesize all accumulated notes and drafts to generate the Discussion and Abstract sections. Sixth step of writer workflow. Requires all notes/*.md files and drafts/introduction.md, methods.md, results.md.