Share FastQC results on GitLab

Question

[pablo]

Hello,

I ran a FastQC analysis and get some results. I would like to share the .html results page on GitLab. The problem is that I downloaded that .html file , and it is located on my C: disk.

I don't know if I can share that file on GitLab in a markdown file in order that other people can see it? And later, I would like to convert that markdown file in a PDF file , with the link of the .html file so that any people around the world can look at it.

Is it possible, and if yes, have you got any suggestion?

Bests

[GenoMax]

FastQC html file is standalone and is meant to be easily sharable as is. Looks like there are html to markdown converters so you could try one of those.

[pablo]

Thanks for your anwer, I am going to check that tool.

When I will have included the FastQC html file into my .md file, and I will have converted that .md file into a .pdf file, anyone would be able to open the link?

[GenoMax]

Access will depend on how you have it set up on your GitLab page.

[pablo]

I understand. But it could be possible to host the FastQC html file and make it visible by everyone?

[GenoMax]

If the page it is on is public then yes. That said you could do this from a simple web link as well.

Answer 1

[Pierre Lindenbaum]

I wrote a minimal/simplistic XSLT stylesheet to convert the output of fastqc to latex/pdf.

It uses the following stylesheet: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/fastqc/fastqc2tex.xsl

Usage:

(cd OUTDIR && unzip jeter_fastqc.zip && cd jeter_fastqc && xsltproc  --stringparam title "${SAMPLE}" path/to/fastqc2tex.xsl fastqc_report.html > jeter.tex &&  pdflatex jeter.tex )

[pablo]

Thanks, I'm gonna check your work.