Nextflow and nf-core tutorial for Genotoul.

Last update: 25/03/2021

This tutorial is largely inspired from material written for the Nextflow Camp 2019, Barcelona 2019-09-19: "Getting started with nf-core" (see programme). Last updated: December 2019

Introduction

What is nf-core?

nf-core is a community-led project to develop a set of best-practice pipelines built using Nextflow. A suite of helper tools aims to help people run and develop pipelines. Actually, 25 pipelines are available for different application such as RNAseq, BSseq, Hi-C, annotation ... It can be used on any computer or cluster without large prerequisites. It's based on nextflow.

What is Nextflow?

Nextflow is :

• a programming language that is designed to manage computational workflows
• and a software that can run a workflow on any infrasctructure.

So, it enables scalable and reproducible scientific workflows using software containers. Nextflow is developed by the Comparative Bioinformatics group at the Barcelona Centre for Genomic Regulation (CRG).

All workflow software dependencies can be embedded into a container.

What are containers?

A container is a standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another. Singularity and Docker are containers system. On HPC such as Genotoul, you can only use Singularity containers.

What this tutorial will cover ?

This tutorial attempts to give an overview of how to use Nextflow command line and nf-core pipelines with singularity: how to run nf-core pipelines, how to understand execution errors, how to configure pipelines, where are my results, how to monitor?

What this tutorial will NOT cover ?

This is NOT a bioinformatic training on a particular workflow. You will NOT learn how to develop a workflow.

Where to get help ?

• about genotoul cluster

Look at our Bioinfo FAQ or Job submission FAQ.

Ask for help with this form.

• about unix command line tldr

One additional tool which this nf-core author swears by is tldr - it gives concise command line reference through example commands for most linux tools, including nextflow, docker, singularity, conda, git and more. There are many clients, but raylee/tldr is arguably the simplest - just a single bash script.

• about nf-core pipelines

The beauty of nf-core is that there are a lot of help on offer! The main place for this is Slack - an instant messaging service. The nf-core Slack organization has channels dedicated for each pipeline, as well as specific topics (eg. #new-pipelines, #tools and #aws).

The nf-core Slack can be found at https://nfcore.slack.com (NB: no hyphen in nfcore!). To join you will need an invite, which you can get at https://nf-co.re/join/slack.