pytest-ngsfixtures documentation¶
About¶
This is a pytest plugin that enables next generation sequencing pytest fixtures, including fastq files and output files from a variety of bioinformatics applications and tools. There are sequencing fixtures for some common sample layouts, but it’s easy to generate additional sample fixture layouts using fixture factories.
- Free software: GNU General Public License v3
Features¶
- a small ngs data set
- predefined sample layouts
- configurable data, reference, and sample fixtures
- wrappers for running shell commands, either in terminals or container applications
- wrappers and helper functions for some workflow engines