A rudimentary pipeline fro processing paired-end reads and aligning them into bam files.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
The nf-core/wgsfastqtobam pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
nf-core/wgsfastqtobam was originally written by Alec Steep & Hongen Xu.