Uploads a multiqc HTML report file to the Viapath Genome Informatics web server. Following this, the app updates the web server index file with a link to the new report.
If required, the data summarised by multiqc is uploaded to the server for trend analysis.
On completion of a sequencing run, this app is run to make multiqc reports available for viewing at [https://genomics.viapath.co.uk/mokaguys/multiqc/]
- An HTML report file generated by multiqc
- Should MultiQC data files be uploaded (boolean, default:True)
- MultiQC data files (Optional)
- old_index.html: The HTML file downloaded from the server by an instance of this app
- new_index.html: The HTMl file generated and uploaded to the server by an instance of this app
Firstly, the app downloads the given input multiqc report. This is copied to the expected location on the server (/var/www/html/mokaguys/multiqc/reports). To connect to the server, this appl requires SSH keys, which are not included in the github repository for privacy reasons. The rsync command is used to perform the copy as it contains a checksum protocol to verify data integrity.
Next, the app adds a link to the top of the server's index.html file, which points to the new multiqc report. The script 'update_index.py' (bundled in a docker image seglh/upload_index) is used to generate this new index. Here, the beautifulsoup4 python module is used for HTML parsing. Below is an example of the HTML string inserted at the top of the report:
<br/>
<div class="well">
<h1>REPORT</h1>
<ul><a href="./reports/REPORT-multiqc.html">MultiQC report</a></ul>
</div>
<br/>
If required, The multiqc data files can be uploaded. First a test is performed to see if the directory already exists (/var/www/html/mokaguys/multiqc/trend_analysis/multiqc_data/runfolder_name). If not, the folder is created and rsync used to copy all files input to this argument to this location.
Developed by Viapath Genome Informatics