Overview

With the increase in the rate at which raw sequencing data is produced due to improved technology and reduced cost of Next-Generation Sequencing (NGS), researchers in the field of bioinformatics and computational biology can perform “multi-omics” data analyses to answer many biological questions. However, analysis of such large datasets comes with a number of challenges, especially when it comes to sharing data analysis methods with the scientific community and being able to reproduce consistent results using the same data across different computational platforms. When it comes to multi-step computational analyses of biological data on a large scale, workflow management systems are an essential component.

Nextflow (https://www.nextflow.io/) is workflow management tool that is gaining significant popularity in the bioinformatics community. Nextflow is a Groovy-based domain-specific language (DSL) specifically designed for Bioinformaticist with a vast programming knowledge to solve many of the challenges of the inability to reproduce data analyses. Some of these challenges are due to computational platform variations, software and database management, complexity of pipelines, intermediate file handling and lack of good practice. Nextflow has a number of features that promote workflow reproducibility, portability and scalability. These include: (1) support for Docker (http://docker.io/) and Singularity/Apptainer (https://www.sylabs.io/), the two most used containerisation software in the bioinformatics community; (2) integration/support for the popular version control system (VCS) GitHub (http://github.com/) for sharing of code and version management; and (3) support for most job schedulers, including Sun Grid Engine (SGE), PBS/Torque, Platform Load Sharing Facility (LSF), Simple Linux Utility for Resource Management (SLURM), HTCondor and Amazon Web Services (AWS), allowing for scaling of computational workflows on HPC and cloud systems. This hands-on seminar will demonstrate the reproducibility, portability and scalability of Nextflow.

Type of training

Virtual Webinar

Date

Intended Audience

This seminar is intended for individuals interested to learn about workflows on nextflow

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