pandoc-crossref not playing nice with header includes

[A A <amine.aboufirass-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>]

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Files test.py

def f(x):
    return x

test.md

~~~{
  #lst:test
  .py
  include="test.py"
  caption=`test.py`
}
~~~

header.tex

\usepackage{minted}

\definecolor{bg}{rgb}{0.85, 0.85. 0.85}
\setminted{breaklines=true, bgcolor=bg, breakanywhere}

Compilation

I’m compiling with:

pandoc -s -F pandoc-crossref -L include-code-files.lua -L minted.lua
-H header.tex --from markdown --to latex test.md -o test.tex
latexmk --shell-escape -pdflatex test.tex

I get an error upon compilation, because pandoc-crossref defines its own
header include which gets overwritten by my -H header.tex. This link
<https://github.com/lierdakil/pandoc-crossref/issues/47> provides more
information.

I tried the solution proposed by @lierdakil in the link provided but get an
error:

! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type H for immediate help.

l.97 $
for(header-includes)$
?

So I’m at a bit of a loss regarding what to do here, Any pointers welcome.
Thanks

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