The nf-core/sarek documentation is split into the following pages:
- Usage
- An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
- Output
- An overview of the different results produced by the pipeline and how to interpret them.
- Input files documentation
- A detailed documentation about the input files.
- Examples
- Different detailes use cases.
- Containers
- Extensive documentation about the containers
- Variant calling
- Detailed documentation on Variant Calling
- ASCAT
- Detailed documentation on ASCAT
- Sentieon
- Detailed documentation on Sentieon
- Snnotation
- Detailed documentation on Annotation
- Reference
- Detailed documentation on the reference used and how to use a custom reference
You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: https://nf-co.re