systemPipeR's
New CWL Command-line Interface

Daniela Cassol ()
Thomas Girke ()

24 June, 2019

Outline

Outline

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

Introduction

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

Drawing

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
Drawing

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Adopting CWL