Paper Template

Reproducible workflow for scientific writing using:

• Markdown for manuscript authoring
• Pandoc for format conversion
• Word DOCX templates for journal submission
• Zotero for live citations
• Lua filters for advanced processing (author affiliations, main/supplement splitting)

Features

• ✅ Automatic author affiliation management with ORCID support
• ✅ Separate main manuscript and supplementary materials from single source
• ✅ Cross-reference supplementary items from main text
• ✅ Flexible figure/table placement (near reference, end of section, or grouped)
• ✅ Table placeholder system for clean manuscripts
• ✅ Automatic figure and table renaming for submission
• ✅ Custom Word template support

Quick Start

1. Add figures to figures/
2. Edit metadata in metadata.yml (authors, affiliations, title)
3. Write manuscript in manuscript.md with table/figure placeholders
4. Build outputs:

   make main        # Build main document
   make supplement  # Build supplementary materials
   make submission  # Rename files for journal submission

Directory Structure

manuscripts/
├── manuscript.md                # Main manuscript source (Markdown)
├── metadata.yml                 # Author/affiliation metadata, Pandoc settings
├── references.bib               # BibTeX bibliography
├── Makefile                     # Build automation
├── template.docx                # Word template for output formatting
├── figures/                     # All figure files (PNG, PDF, JPG)
├── tables/                      # Optional: pre-formatted tables (if not using placeholders)
│   └── tables.yml               # Optional: maps table IDs to DOCX files
├── filters/                     # Pandoc Lua filters for processing
│   ├── author-info-blocks.lua   # Format author/affiliation blocks
│   ├── scholarly-metadata.lua   # Normalize author metadata
│   ├── split-main-supp.lua      # Split main/supplement sections
│   ├── supp-numbering.lua       # Add "Figure SX" prefixes to captions
│   ├── table-docx-refs.lua      # Handle table div references
│   └── resolve-supp-refs.lua    # Convert supp refs to "SX" format
├── scripts/                     # Helper scripts
│   └── rename_for_submission.py # Rename files for journal submission
├── styles/                      # Citation styles
│   └── nature.csl               # Nature journal citation style
└── build/                       # Generated outputs (created by make)
    ├── main.docx
    ├── supplement.docx
    └── submission/              # Renamed files for submission

Requirements

• Pandoc ≥ 2.19
• Python ≥ 3.7
• Make
• PyYAML (pip install pyyaml)

Author Metadata

Authors and affiliations are managed in metadata.yml with support for:

• Multiple affiliations per author
• ORCID identifiers
• Corresponding and equal-contributor markers
• Email addresses

Documentation

• USAGE.md - Comprehensive usage guide with examples
• filters/README.md - Detailed filter documentation and pipeline explanation

License

MIT License - see LICENSE file for details