Question: Converting MultiQC Reports to PDF
gravatar for serodyc
11 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 • 585 views
ADD COMMENTlink modified 8 months ago by Michael Dondrup46k • written 11 months ago by serodyc10

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

ADD REPLYlink written 11 months ago by Pierre Lindenbaum122k
gravatar for Phil Ewels
8 months ago by
Phil Ewels430
Sweden / Stockholm / SciLifeLab
Phil Ewels430 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 8 months ago by Phil Ewels430
gravatar for jrj.healey
11 months ago by
United Kingdom
jrj.healey13k 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 11 months ago by jrj.healey13k
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