Question: Converting MultiQC Reports to PDF
gravatar for serodyc
22 months ago by
serodyc10 wrote:

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?

multiqc pdf • 1.1k views
ADD COMMENTlink modified 6 months ago by joe5550 • written 22 months ago by serodyc10

duplicate of Fastqc Html Report To Pdf (With A Script)

ADD REPLYlink written 22 months ago by Pierre Lindenbaum129k
gravatar for Phil Ewels
19 months ago by
Phil Ewels560
Sweden / Stockholm / SciLifeLab
Phil Ewels560 wrote:

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). 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)_

ADD COMMENTlink written 19 months ago by Phil Ewels560
gravatar for Joe
22 months ago by
United Kingdom
Joe17k wrote:

According to their docs it supports output in PDF natively, though you need Pandoc installed.

Otherwise you may be able to convert it yourself with Pandoc.

ADD COMMENTlink written 22 months ago by Joe17k
gravatar for joe555
6 months ago by
joe5550 wrote:

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.

ADD COMMENTlink written 6 months ago by joe5550
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