### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2009

@dragonstyle You should read to the bottom of the discussion to see the clearest explanation of what the bug is.

<div type='discussions-op-text'>

<sup>Originally posted by **sammo3182** August 19, 2022</sup>
Recently I asked a question about varying the reference allocation with Quarto in #1728. Then I find the problem that made the old rmarkdown tricks not work was because I used the [`article-format-template`](https://github.com/quarto-journals/article-format-template). The reference was in the right place I want when rendering the plain pdf but then moved to the very end of the document when rendering the `aft`. 

A replicable example:

```qmd
---
format:
  pdf:
    number-sections: true
  aft-pdf:
    keep-tex: true  
  aft-html: default

bibliography: bio.bib
title:  A test
---

content @Hu2020

# Reference

::: {#refs}
:::

# Online Supplementary Materials

```
[bio.zip](https://github.com/quarto-dev/quarto-cli/files/9386033/bio.zip)

See the difference of the reference when choosing the following options respectively:

![image](https://user-images.githubusercontent.com/6463211/185724871-cd89a2f3-24d7-4787-8515-d2aba80475e6.png)


How could I allow the `aft` to recognize my reference setting? Any suggestion will be very helpful.
Moreover, a more detailed instruction and examples about how to customize the template than the current [brief version](https://github.com/quarto-journals/article-format-template/blob/main/README.md) under aft repo and Quarto.org will be super welcomed---details like how to arrange the author area, showing the corresponding author, adding the key words and acknowledge, etc.</div>
dragonstyle
2022-08-21T13:04:30Z
jjallaire
v1.4
open
Varying the reference position in `quarto-journals` template
https://github.com/quarto-dev/quarto-cli/issues/2024