### Bug description

This report describes an issue with obtaining bibliographic data directly from Zotero, bypassing the need for exporting `.bib`, `.json`, or `.yaml` bibliographic data, by using the Zotero add-on [zotxt](https://github.com/egh/zotxt) and the associated pandoc filter [pandoc-zotxt.lua](https://github.com/odkr/pandoc-zotxt.lua/).

**Using Rmarkdown**, it is possible to knit/render files such as the following from within RStudio (provided Zotero is running, and an entry `@bard:2015introduction` does exist):

```
---
output:
  html_document: 
    pandoc_args:
      - '--lua-filter'
      - pandoc-zotxt.lua
      - '--citeproc'
---

Blah blah [@bard:2015introduction, 67].
```

Result:

> Blah blah (Bard 2015, 67).

> Bard, Kathryn A. 2015. *An Introduction to the Archaeology of Ancient Egypt.* 2nd ed. Hoboken, NJ: Wiley-Blackwell.

**Using quarto from the command line**, with this file (`test.qmd`)

```
---
format: html
---

Blah blah [@bard:2015introduction, 67].
```

and the command

```
quarto render test.qmd -L /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua -C
```

produces the exact same expected result.

(Note that I had to provide the full path to the filter here, but that seems to be a different issue.)

For **`qmd` from within RStudio**, one would expect to be able to achieve the same with appropriate settings in the YAML metadata block;  however, this does not seem to be possible, as using `pandoc-args` (or `pandoc_args`) has no effect, and [does not seem to be supported anyway](https://github.com/quarto-dev/quarto-cli/discussions/630).

Example:

```
---
format:
  html: 
    pandoc-args:
      - '--lua-filter'
      - /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
      - '--citeproc'
---

Blah blah [@bard:2015introduction, 67].
```


Result:

> Blah blah [@bard:2015introduction, 67].

(i.e., citation not resolved)


Including `filters` and `citeproc: TRUE` in the header has no effect either:

```
---
filters:
  - /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
citeproc: TRUE
format: html
---

Blah blah [@bard:2015introduction, 67].
```

Result:

> Blah blah [\@bard:2015introduction, 67].

(i.e., citation not resolved)


What does work is including the instruction to use a bibliography file (`dummy.json`) which includes only one (dummy) entry, different from `@bard:2015introduction`. This seems sufficient to trigger the activation of `citeproc`.

```
---
filters:
  - /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
format: html
bibliography: dummy.json
---

Blah blah [@bard:2015introduction, 67].
```

Result: as expected (note that not even `citeproc: TRUE` is required here).

**Possible solutions:**

1. Allow the use of `citeproc` as a (pseudo-) filter (note that the the order of filters matters)

	```
	filters:
	  - /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
	  - citeproc
	```
2. Include support for using `pandoc-args` (or `pandoc_args`) in a YAML metadata block.
3. Make the following work:

	```
	filters:
	  - /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
	citeproc: TRUE
	```
	
	A problem I see here, though, is that in this particular case `pandoc-zotxt.lua` has to be run before `citeproc`, but there might be other filters that have to be run after `citeproc`, so the option to force a specific order of filters (and pseudo-filters) which would be possible with 1. and 2.  might be best.


---

RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 11_6_8) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36

quarto -v
1.1.179



### Checklist

- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
cscheid
2022-09-05T08:51:16Z
njbart
bug
closed
citeproc settings in YAML metadata block: Problems when using pandoc-zotxt.lua filter
https://github.com/quarto-dev/quarto-cli/issues/2294