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.
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.
The NIPT scripts require a .niptrc file to be placed in the excuting user's $HOME
. A template has been provided.
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
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.
Please check out our guide for contributing to demultiplexing