This application is used for samplesheet generation and parsing at the next generation sequencing core facility Center for Translational Genomics (CTG). It will, given a csv file, create a samplesheet that can both be used for demultilexing with bcl-convert, and further downstream analysis with our meta pipelines Yggdrasil.

In order to start the application, make sure that you have docker, docker compose, and git installed. Then run the following:

git clone https://github.com/ctg-lund/SampleSheetGenerator
cd SampleSheetGenerator
docker-compose up

Then navigate to localhost:8082/samplesheet.

The tech stack is based on three main technologies:

• Flask
  • For building the actual web application which can process user data and return a validated samplesheet in pure python (with a little jinja sprinkled on top)
• Gunicorn
  • For a production grade wsgi, instead of flask's built-in wsgi which isn't meant to be in production
• Pandas
  • For easier parsing and handling of csv data, used in the "backend" of the application.

The application is built with the intention to be deployed behind a proxy apache2 server. For more information on how to deploy on a apache server, look here!

Form updated main script takes index kit from form

• add indexes to samplesheet
• add fields to replace a well with the index pair of another well
• strip unnecessary info from illumina v2
• start from a simple csv table with just sample names filled in