| name | pandoc-docx |
| description | Create clean Word documents (.docx) from Markdown using pandoc, automatically applying the bundled NIH-style reference template (Arial 11pt, 1-inch margins, single-spacing, NIH heading hierarchy) so manuscripts, abstracts, and grant attachments come out grant-ready by default. Use when the user asks to create a new Word document from fresh Markdown content (manuscript draft, NIH grant attachment, abstract, specific aims page, biosketch). Do NOT use this skill to revise an existing .docx with tracked changes — that is `docx-review`'s job. |
pandoc-docx
Create clean first-draft Word documents from Markdown with pandoc. The skill ships a bundled NIH-formatted reference template at assets/nih-reference.docx and applies it automatically unless the user explicitly overrides with --reference-doc.
When to use this skill (vs. docx-review)
| Task | Skill |
|---|
| "Create a Word document from this outline / markdown" | pandoc-docx |
| "Generate a clean manuscript draft in .docx" | pandoc-docx |
| "Convert this NIH specific-aims markdown into the right format" | pandoc-docx |
| "Add tracked changes to this .docx" | docx-review |
| "Respond to the reviewer's comments in the .docx" | docx-review |
| "Diff these two .docx files" | docx-review |
Rule of thumb: if a .docx doesn't exist yet, use this skill. If it does and the user wants edits visible to a reviewer, use docx-review.
Install (workspace)
pandoc is the only required dependency. The Coder workspace's startup script
installs it; if missing:
brew install pandoc
The NIH reference template is bundled at assets/nih-reference.docx (this skill's directory). Treat that path as canonical — do not regenerate or modify.
Default workflow
NIH_REF="$(dirname "$0")/assets/nih-reference.docx"
NIH_REF=~/.codex/skills/pandoc-docx/assets/nih-reference.docx
pandoc manuscript.md \
--reference-doc="$NIH_REF" \
-o manuscript.docx
open manuscript.docx
xdg-open manuscript.docx
Output is clean (no tracked changes) by default.
NIH formatting baked into the template
The reference template at assets/nih-reference.docx enforces NIH grant-application formatting:
| Property | Value | Source |
|---|
| Font | Arial | NIH grant guide |
| Size | 11 pt | NIH grant guide |
| Line spacing | Single | NIH grant guide |
| Margins | 1 inch on all sides | NIH minimum 0.5" |
| Page size | US Letter (8.5 × 11") | NIH default |
| Heading hierarchy | H1 → H2 → H3 with NIH style IDs | template-defined |
The template defines 49 named styles (Heading1–Heading3, Abstract, AbstractTitle, BodyText, Bibliography, Caption, FirstParagraph, FootnoteReference, etc.) — pandoc uses them automatically based on Markdown structure (# → Heading1, ## → Heading2, blockquotes → BlockText, etc.).
NIH guide reference: https://grants.nih.gov/grants/how-to-apply-application-guide/format-and-write/format-attachments.htm
Common patterns
Manuscript draft
pandoc manuscript.md \
--reference-doc=$(dirname "$0")/assets/nih-reference.docx \
--toc \
-o manuscript.docx
NIH Specific Aims page (single page)
pandoc specific-aims.md \
--reference-doc=$(dirname "$0")/assets/nih-reference.docx \
-o specific-aims.docx
Abstract (250 words, single block)
pandoc abstract.md \
--reference-doc=$(dirname "$0")/assets/nih-reference.docx \
-o abstract.docx
With a bibliography (CSL JSON or BibTeX)
pandoc manuscript.md \
--reference-doc=$(dirname "$0")/assets/nih-reference.docx \
--citeproc \
--bibliography=refs.bib \
--csl=american-medical-association.csl \
-o manuscript.docx
User wants a non-NIH layout
If the user passes their own --reference-doc, respect that override — do not silently re-apply the NIH template. They may need a journal-specific template (e.g., Cell, JAMA).
Markdown conventions that round-trip cleanly
| Markdown | Word output |
|---|
# Title | Heading 1 (Arial 14pt bold) |
## Section | Heading 2 (Arial 12pt bold) |
### Subsection | Heading 3 (Arial 11pt bold italic) |
**bold** | Bold |
*italic* | Italic |
> quote | BlockText style |
1. item / - item | Numbered/bulleted list |
[link](url) | Hyperlink |
[@cite2024] (with --citeproc) | Formatted in-text citation |
 | CaptionedFigure with auto-caption |
What this skill does NOT do
- Tracked changes / comments / revisions: that is
docx-review's job. Do not try to insert <w:ins> or <w:del> markup with pandoc; the output won't be valid.
- Specific NIH form attachments (R&R Cover, PHS Assignment Request, etc.): those are PDF forms downloaded from the NIH website and filled with Adobe Acrobat. Pandoc cannot generate them.
- Endnote field-code references: pandoc emits inline citations or a Bibliography section, not Endnote XML field codes. If the user needs
{HYPERLINK...} Endnote fields, use cliproxy's research-pipeline endnote generator.
Troubleshooting
| Symptom | Cause | Fix |
|---|
| "pandoc: not found" | not installed in workspace | brew install pandoc (or rerun the workspace startup script) |
| Output looks like Calibri 11pt, not Arial | --reference-doc not passed or path wrong | check ls $(dirname "$0")/assets/nih-reference.docx resolves; pass an absolute path if invoking from a non-script context |
| Headings render as plain bold text | Markdown source uses **Section** instead of ## Section | rewrite as ATX-style headings |
--citeproc warns "no bibliography" | --bibliography flag missing | add --bibliography=refs.bib |
References
references/cookbook.md — copy-paste-ready recipes (manuscript, specific aims, abstract, with bibliography)- Bundled template:
assets/nih-reference.docx
- Pandoc DOCX docs: https://pandoc.org/MANUAL.html#docx
