Render notebooks that are not embedded within the index.qmd in a manuscript project

[cyrilcros]

What would you like to do?

Give feedback or suggest an improvement

Description

Hi, I am trying to use a manuscript following https://quarto.org/docs/manuscripts/ with a separate notebooks folder. I am confused about the documentation for the following:

• is it possible to force rendering some notebooks even if I don't use any links to them in my index.qmd? Let's I have a notebook about data loading and cleaning up I directly save.
• is it possible to render the notebooks as PDF?

To be clear, let's say I have a Github repo like https://github.com/cejuliano/hydra_single_cell (not my work) with Rmd and PDFs.
I would like to be able to write an overall supplementary materials PDF (the index.qmd) with supplementary figures and tables from notebooks, plus render and execute notebooks that are not linked because they are used to do basic processing or produce PDF figures for the main article text I am doing elsewhere.

On v1.4:
Using manuscript: notebooks: - notebook: notebooks/-please-render-this-notebook.qmd does not work.
Using quarto render notebooks/ --to pdf does not work.

Thanks for your help and understanding!

[mcanouil]

For questions, please use the Q&A discussions: https://github.com/quarto-dev/quarto-cli/discussions/new?category=q-a

I'm converting this to one.

Sharing a repository which is not yours, big and unrelated to Quarto is not useful to understand your setup and what you are trying to achieve.
Could you share a small self-contained "working" (reproducible) example to work with, i.e., a complete Quarto document or a Git repository? The goal is to make it as easy as possible for us to recreate your problem so that we can fix it: please help us help you! Thanks.

Finally, if "On v1.4:" means you are using Quarto CLI 1.4, please upgrade to 1.7.30.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code block (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.