One metagenome pipeline to rule them all - this nextflow pipeline is a complete end-end metagenomic solution creating visulations of taxonomic data from fastq input files, by utilising plass and mmseq tools

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 / singularity containers making installation trivial and results highly reproducible.

The nf-core/onemetagenome pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting