Question: Share FastQC results on GitLab
0
gravatar for vincentpailler
7 days ago by
vincentpailler140 wrote:

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

gitlab markdown html fastqc • 68 views
ADD COMMENTlink modified 7 days ago by Pierre Lindenbaum129k • written 7 days ago by vincentpailler140

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.

ADD REPLYlink modified 7 days ago • written 7 days ago by genomax85k

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?

ADD REPLYlink written 7 days ago by vincentpailler140

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

ADD REPLYlink written 7 days ago by genomax85k

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

ADD REPLYlink written 7 days ago by vincentpailler140

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

ADD REPLYlink written 7 days ago by genomax85k
0
gravatar for Pierre Lindenbaum
7 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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 )
ADD COMMENTlink written 7 days ago by Pierre Lindenbaum129k

Thanks, I'm gonna check your work.

ADD REPLYlink written 7 days ago by vincentpailler140
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