demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline

There are two parts to this package: a pure bash part and a python package.

Bash

All workflow related scripts are written in bash. They will set up the right environment to allow for easy demulitplexing and moving data around between locations and servers.

• demux.bash: the main script demultiplexing Illumina HiSeq2500 data (bcl2fastq).
• *nipt.bash: scripts enabling NIPT data processing.
• hiseqx/x*.bash: scripts for demultiplexing Illumina HiSeqX data (bcl2fastq).

NIPT

The NIPT scripts require a .niptrc file to be placed in the excuting user's $HOME. A template has been provided.

python

All SampleSheet related actions are bundled in a python package enabling easier testing.

$ demux sheet --help
Usage: demux sheet [OPTIONS] COMMAND [ARGS]...

  Samplesheet commands

Options:
  --help  Show this message and exit.

Commands:
  demux     Convert a machine samplesheet for demux
  fetch     Fetch a samplesheet from LIMS
  massage   create a NIPT ready SampleSheet
  validate  validate a samplesheet

Installation

You can install demultiplexing via pip

pip install demux

or via poetry:

$ git clone https://github.com/Clinical-Genomics/demultiplexing && cd demultiplexing
poetry install
poetry run demux

You also need a YAML config file describing how to connect to the LIMS instance. It should contain information like this:

---
host: https://genologics.mycompany.com
username: apiuser
password: somepassword

Files will be blacked automatically with each push to github. You can use pre-commit if you would like to automatically Black format your commits on your local machine before pushing to github. Pre-commit is installed using:

pre-commit install

Precommit will then use the .pre-commit-config.yaml and run the pre-commit hooks defined there before committing the results.

Contributing

Please check out our guide for contributing to demultiplexing