Cloud Pipelines with Terra and Workflow

Cloud Pipelines with Terra and Workflow

Cloud-based bioinformatics pipelines have revolutionized large-scale genomics research by providing scalable, reproducible, and collaborative computational environments. This course provides comprehensive training on cloud computing workflows using the Terra platform, emphasizing workflow automation, data management, and integration with high-throughput sequencing datasets. Participants begin with an introduction to cloud computing concepts, Terra platform architecture, and its relevance in genomics and bioinformatics. The course emphasizes secure data handling, collaborative analysis, and reproducible workflow management using the Workflow Description Language (WDL) and Common Workflow Language (CWL). Core modules cover launching and managing cloud workspaces, importing and organizing datasets, designing and executing computational workflows, monitoring pipeline performance, and troubleshooting errors. Hands-on exercises involve running pipelines for RNA-Seq, DNA-Seq, variant calling, and multi-omics data analysis using Terra and integrating results with downstream bioinformatics tools. Advanced topics include workflow optimization, parallelization, cost-effective resource management, workflow versioning, data provenance, integration with GitHub and Dockstore, and automated reporting. Participants explore best practices for compliance, reproducibility, and FAIR principles in cloud-based genomics research. Case studies highlight collaborative projects in population genomics, cancer research, single-cell analysis, and multi-omics integration, demonstrating the efficiency gains and reproducibility advantages of cloud-based workflows. By the end of this course, participants will be able to design, implement, and manage cloud-based bioinformatics pipelines on Terra, automate multi-step workflows, handle large-scale datasets securely, optimize resource usage, ensure reproducibility and transparency, integrate pipelines with other bioinformatics tools, and communicate findings effectively. This training equips bioinformaticians, computational biologists, and genomics researchers with essential skills to leverage cloud infrastructure for scalable and reproducible analyses.

Syllabus

• Module 1: Introduction to Cloud Computing for Genomics
• Module 2: Overview of Terra Platform and Workspaces
• Module 3: Workflow Design with WDL and CWL
• Module 4: Data Import, Management, and Organization
• Module 5: Running RNA-Seq, DNA-Seq, and Variant Calling Pipelines
• Module 6: Troubleshooting and Pipeline Optimization
• Module 7: Parallelization and Cost Management
• Module 8: Workflow Versioning and Data Provenance
• Module 9: Integration with GitHub, Dockstore, and Downstream Tools
• Module 10: Case Studies, Reproducibility, and Best Practices

Prerequisites

Basic knowledge of bioinformatics workflows, genomics data, and command-line computing; familiarity with R or Python

Learning Outcomes

Design and execute cloud-based bioinformatics pipelines; Manage and organize large-scale datasets; Automate workflows using WDL and CWL; Optimize computational resources; Implement reproducible and collaborative analysis; Integrate pipelines with downstream tools; Communicate results effectively

Certificate

Participants who successfully complete the training program will be awarded an official Certificate of Completion issued by Helix Institute for Medical & Biological Sciences LLC (USA).
The certificate confirms that the participant has attended and fulfilled the academic and practical requirements of the course, including lectures, workshops, assignments, and assessments, where applicable.
Each certificate includes:

• Full name of the participant
• Duration and total instructional hours
• Date of completion
• Title of the training program
• Official signature of the authorized representative of Helix Institute
• Institutional logo and identification number (Certificate ID)
• Verification reference for authenticity

Certificates issued by Helix Institute are designed to support professional development, academic portfolios, and continuing education records. Participants may use the certificate as evidence of specialized training in biomedical and life sciences disciplines.
For selected programs, certificates may also be issued in collaboration with partner institutions, universities, or scientific organizations when applicable.
Helix Institute maintains records of issued certificates to ensure verification and transparency. Employers, academic institutions, and professional organizations may request confirmation of certificate authenticity through official communication with the Institute.
Certificates are delivered electronically in secure digital format upon successful completion of the program. Printed certificates may be issued upon request.