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Convert to Markdown

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Aaron Wolen edited this page Aug 20, 2020 · 2 revisions

A few notes on converting notebooks to Markdown suitable for importing to GitBook.

pandoc \
  -fipynb \
  -tmarkdown-raw_html-native_divs-fenced_divs \
  --ipynb-output=all \
  --atx-headers \
  genomics/02-vcf-python.ipynb -o 02-vcf-python.md

setting --ipynb-output to all causes Pandas dataframes to be included as both HTML tables and plain text code blocks. Since GitBook doesn't understand HTML, the HTML tables should be deleted.
Disabling the div and raw html extensions removes the fenced divs containing cell metadata.