data_note_pandoc

Pandoc filters, templates, and wrapper scripts for converting genome note Markdown files to docx, pdf and JATS-XML files.

Dependencies

• Pandoc 3.x
• pandoc-crossref
• panflute (pip install panflute)
• XeLaTeX (for PDF output)

Usage

All scripts take the input .md file as the first argument and derive the output filename automatically. An explicit output path can be given as a second argument.

# PDF via XeLaTeX
bin/gn-pdf ilActPoly1.md

# DOCX for review (figures and tables inline)
bin/gn-docx-review ilActPoly1.md

# DOCX for submission (figures and tables at end)
bin/gn-docx-sub ilActPoly1.md

# JATS XML for Wellcome Open Research
bin/gn-jats ilActPoly1.md

Filter order

Filter order matters and must not be changed.

JATS pipeline:

1. normalize_pandoc_inputs.lua — rewrites BibTeX italic markers; promotes table IDs
2. pandoc-crossref — resolves @fig: / @tbl: cross-references
3. fix-figtbl-xref.py — converts figure/table elements to raw JATS blocks
4. --citeproc — processes citations using BibTeX input and CSL
5. JATS writer using Pandoc and an XML template
6. postprocess-jats.py — sorts references, adds punctuation, restores italics

DOCX submission pipeline:

1. inject_frontmatter.lua — injects styled author/affiliation/grant block
2. pandoc-crossref
3. extract_figs_tables.lua — moves figures and tables after references
4. --citeproc

DOCX review pipeline: same as submission but without extract_figs_tables.lua.

PDF pipeline: pandoc-crossref → --citeproc → XeLaTeX.

Repository layout

bin/          wrapper scripts (gn-pdf, gn-docx-review, gn-docx-sub, gn-jats)
filters/      Lua and Python Pandoc filters
templates/    LaTeX template, JATS-XML template, DOCX reference doc, CSL, fonts