/meteor_pipeline

A wrapper for the automation and parallelisation of METEOR and its downstream analysis

Primary LanguageRGNU General Public License v3.0GPL-3.0

Introduction

A nextflow wrapper for the automation and parallelisation of the METEOR pipeline and its downstream analysis. Release of the pipeline onto nf-core is under development. Uppmax and Rosalind HPC's are the only tested environments for the pipeline.

Uppmax Quick Start

  1. Load Nextflow according to the "nf-core configuration" (>=20.07.1)

  2. Download the pipeline and test it on the nf-mag minimal dataset of paired end illumina reads by modifying the conf/upprun.config file.

  3. Run on the uppmax HPC cluster with a single command:

nextflow run main.nf\
	-c configs/institutional/uppmax.config\
	-c configs/conf/upprun.config

Acknowledgements

  • INRA
  • SciLifeLab
  • KCL
  • KTH