Black in ComBio Workshop Series - Introduction to Command line and Seqera Workflows

September 27th:

Command Line for Bioinformatics

Unlock the power of the command line in our hands-on workshop tailored for members of our online community! Join Dr. Rhondene Wint, a seasoned expert in bioinformatics, for an insightful introduction to the command line interface (CLI) and its applications in bioinformatics.

In this workshop, you will:

• Discover the Shell: Gain a foundational understanding of the command line interface, exploring its capabilities and how it streamlines data management and analysis tasks in bioinformatics.
• Navigate Directories: Learn essential skills for navigating directories and managing files using command-line commands. Mastering these techniques will enhance your efficiency in handling large datasets and performing complex operations.
• Explore Genomic File Types: Get introduced to various genomic file types commonly used in bioinformatics. Understand their formats, purposes, and how to interact with them using the command line.

October 17th and 18th:

Getting started with workflows for bioinformatics

Nextflow is a powerful and flexible open-source workflow management system that simplifies the development, execution, and scalability of data-driven computational pipelines. It's widely used in bioinformatics and other scientific fields to automate complex analyses, making it easier to manage and reproduce large-scale data workflows.

This is a foundational course for those who are completely new to Nextflow. It aims to equip participants with skills in two key areas: Nextflow language proficiency and command-line interface (CLI) execution.

Participants will be guided through hands-on, goal-oriented exercises that will allow them to develop the following skills:

• Use core components of the Nextflow language to construct simple multi-step workflows effectively.
• Launch Nextflow workflows locally, navigate output directories to access results, interpret log outputs for insights into workflow execution, and troubleshoot basic issues that may arise during workflow execution.

By focusing on these essential skills, participants will be well-prepared to harness the power of Nextflow for their scientific computing needs.

Instructors: Geraldine Van der Auwera and Ken Brewer, developer advocates at Seqera

This is a workshop for people who are completely new to Nextflow. Basic familiarity with the command line, and common bioinformatics file formats is assumed.