NeeluBegum / meteor_pipeline

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

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