systemPipeR's
New CWL Command-line Interface
24 June, 2019
Outline
- Introduction
- 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
.