Note: This repository has been archived and consolidated into: https://github.com/pepkit/pep-pipelines/

This repository aims to show users how to run nf-core pipeline with PEP as input, using taxprofiler pipeline as an example.

The command would look something like that:

nextflow run nf-core/taxprofiler -profile test_pep --outdir /home/cgf8xr/nextflow-output