Outline

• Introduction
  • Motivation
  • systemPipeR
• Design
• Getting started
• Workflow Demonstration

Motivation

• Many NGS applications share several analysis routines, such as:
  • Read QC and preprocessing
  • Alignments
  • Quantification
  • Feature annotations
  • Enrichment analysis
• Thus, a common workflow environment has many advantages for improving efficiency, standardization and reproducibility
  

Common Workflow Environment: Requirements

• Design and execution of end-to-end analysis pipelines
• Support for R and command-line software
• Runs on single machines and compute clusters
  
• Uniform interface across different data analysis applications
• Uniform sample handling and annotation
• Automated report generation
• Flexibility to support custom changes and new software/tools

systemPipeR

• systemPipeR is an R package for building end-to-end analysis pipelines with automated report generation for data analysis applications
  

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Adopting CWL