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I am trying to convert a txt file (markdown) to docx using pandoc with a special MS Word template. I'm doing it this way:

pandoc -s --reference-docx=/path/to/my/template.dotx -o outfield.docx file.md

The problem is that I have set up my template with a special "Body Paragraph" style, separate from the "Normal" style (because the various headings, etc. all are based on the "Normal" style. Is there a way to tell pandoc that when it converts normal paragraph text that it should be styled using my special "Body Paragraph" style?

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pandoc 1.19.2.1 uses three styles for body text: Normal, Body Text, and First Paragraph, which are based onto each other in this order. If you want a specific styling of your body text only, you should hence edit the Body Text style in the template, not the Normal style as changes to the Normal style -- as you already mentioned -- propagate to other styles as well.

See the part on the --reference-docx option in the 'Options Affecting Specific Writers' section of the pandoc user manual.

This feature might exist pre-1.19.2.1 version, I don't know when this has been introduced.

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