I am having trouble converting some MultiQC reports from HTML to PDF format while preserving the files' graphics.  I am working on a Red Hat Linux cluster and trying to accomplish this with a Bash script.  Currently, I have tried using several versions of wkhtmltopdf to do this, and, although it converts the files, the graphs and charts are not rendered.  For example, the charts for where my Sequence Quality Histograms or Per Sequence Quality Scores should be will instead have a gray box with the text "loading..." inside.  Has anyone found a tool that works for this?  
The problem is that MultiQC plots are by default rendered as interactive JavaScript objects. These aren't traditional graphics and tend to not do well with HTML conversion tools such as the one you're trying. MultiQC can render static image plots though, using the option `--flat`. There's also a template called "simple" (use `-t simple`) which produces a report with no JavaScript at all.

The `--pdf` option renders a HTML report using the simple template and then passes this through the pandoc command (see the command [here](https://github.com/ewels/MultiQC/blob/44cf7ea9c8b153be1baebec76ebba0370aad8333/scripts/multiqc#L700-L709)). It's a little flaky as it requires you to install pandoc yourself, which can vary quite a bit between systems. It is something that could potentially be dropped in future versions of MultiQC.

Generally when people ask about PDF conversion I ask "Why?". I'm always curious - what's the use case here?

Phil _(author of MultiQC)_