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?
--flat. There's also a template called "simple" (use
Generally when people ask about PDF conversion I ask "Why?". I'm always curious - what's the use case here?
Phil _(author of MultiQC)_
If you have already generated a regular MultiQC html report, and you are not able to rerun MultiQC again for any reason, you can convert it to pdf using the Opera browser. Save it directly into pdf instead of printing it. (One use case would be if you are asked to actually print at least some of your results.) Surely, if htmldoc / pandoc on the command line works for the conversion, then it is the way to go.