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CTG Samplesheet Generator

Introduction

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.

Quick start

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.

Technical description

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!

Updates

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