Nextflow: Reproducible Containerised Scientific Workflows across Clusters and Cloud

Dates

12-14 April 2021

Due to the COVID-19 outbreak, this course will be held online

Overview

 

Nextflow is a widely adopted workflow system for running high-throughput, data-intensive applications across cloud and on-premise infrastructure. 
It has fast become one of the primary technology platforms for computational workloads in life sciences.
The framework allows scientists to write code in any scripting language, define software dependencies with containers, connect tasks with the event-driven dataflow programming DSL and then deploy anywhere: local machines, grid computing systems or public cloud infrastructure.

Target audience and assumed background

 

The workshop is intended for users to become quickly proficient in Nextflow technology, starting from basic through to advanced concepts. 
Intensive training is provided across 14 Nextflow topics with each topic designed to last between 45 to 60 min and includes talks, live demonstrations and practical sections which all participants can complete. 

 

Program

Monday- Classes from 3-6 pm CET

 

  • Overview of Nextflow workflow system
  • Nextflow language syntax and data structures
  • Dataflow variables and channel semantics
  • Nextflow operators and processes
  • Simple pipeline implementation

 

Tuesday- Classes from 3-6 pm CET

  • Modules and DSL2
  • Pipeline sharing & best practice for reproducibility
  • Nextflow configuration and profiles
  • Managing dependencies with containers
  • Executors & deployment scenarios

 

Wednesday- Classes from 3-6 pm CET

  • Error recovery & strategies for error handling
  • Workflow and runtime metadata and events
  • Common implementation patterns
  • Implementation of a variant calling pipeline

 

A repository will be provided with all the necessary material and software as well as an AWS cloud environment to carry out the activities in the relevant practical sessions.

Instructors

 

Dr. Paolo Di Tommaso

 

 

 

 

 

COst overview

Package 1

 

 

  350 €


Cancellation Policy:

 

 

 

> 30  days before the start date = 30% cancellation fee

 

< 30 days before the start date= No Refund.

 

 

 

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.