Introduction

Note: if you use {systemPipeR} in published research, please cite: Backman, T.W.H and Girke, T. (2016). systemPipeR: NGS Workflow and Report Generation Environment. BMC Bioinformatics, 17: 388. >10.1186/s12859-016-1241-0.

systemPipeR(SPR) provides flexible utilities for designing, building and running automated end-to-end analysis workflows for a wide range of research applications, including next-generation sequencing (NGS) experiments, such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq (H Backman and Girke 2016). Important features include a uniform workflow interface across different data analysis applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters (Figure 1). The latter supports interactive job submissions and batch submissions to queuing systems of clusters.

systemPipeR has been designed to improve the reproducibility of large-scale data analysis projects while substantially reducing the time it takes to analyze complex omics data sets. It provides a uniform workflow interface and management system that allows the users to run selected workflow steps, as well as customize and design entirely new workflows. Additionally, the package take advantage of central community S4 classes of the Bioconductor ecosystem, and enhances them with command-line software support.

The main motivation and advantages of using systemPipeR for complex data analysis tasks are:

  1. Design of complex workflows involving multiple R/Bioconductor packages
  2. Common workflow interface for different applications
  3. User-friendly access to widely used Bioconductor utilities
  4. Support of command-line software from within R
  5. Reduced complexity of using compute clusters from R
  6. Accelerated runtime of workflows via parallelization on computer systems with multiple CPU cores and/or multiple nodes
  7. Improved reproducibility by automating the generation of analysis reports

Relevant features in `systemPipeR`. Workflow design concepts are illustrated under (A). Examples of `systemPipeR's` visualization functionalities are given under (B).

Figure 1: Relevant features in `systemPipeR`. Workflow design concepts are illustrated under (A). Examples of `systemPipeR's` visualization functionalities are given under (B).

A central concept for designing workflows within the systemPipeR environment is the use of workflow management containers. Workflow management containers facilitate the design and execution of complex data analysis steps. For its command-line interface systemPipeR adopts the widely used Common Workflow Language (CWL) (Amstutz et al. 2016). The interface to CWL is established by systemPipeR's workflow control class called SYSargsList (see Figure 2). This design offers many advantages such as: (i) options to run workflows either entirely from within R, from various command-line wrappers (e.g., cwl-runner) or from other languages (, e.g., Bash or Python). Apart from providing support for both command-line and R/Bioconductor software, the package provides utilities for containerization, parallel evaluations on computer clusters and automated generation of interactive analysis reports.

Overview of `systemPipeR` workflows management instances. A) A typical analysis workflow requires multiple software tools (red), as well the description of the input (green) and output files, including analysis reports (purple). B) `systemPipeR` provides multiple utilities to design and build a workflow, allowing multi-instance, integration of R code and command-line software, a simple and efficient annotation system, that allows automatic control of the input and output data, and multiple resources to manage the entire workflow. c) Options are provided to execute single or multiple workflow steps, while enabling scalability, checkpoints, and generation of technical and scientific reports.

Figure 2: Overview of `systemPipeR` workflows management instances. A) A typical analysis workflow requires multiple software tools (red), as well the description of the input (green) and output files, including analysis reports (purple). B) `systemPipeR` provides multiple utilities to design and build a workflow, allowing multi-instance, integration of R code and command-line software, a simple and efficient annotation system, that allows automatic control of the input and output data, and multiple resources to manage the entire workflow. c) Options are provided to execute single or multiple workflow steps, while enabling scalability, checkpoints, and generation of technical and scientific reports.

An important feature of systemPipeR's CWL interface is that it provides two options to run command-line tools and workflows based on CWL. First, one can run CWL in its native way via an R-based wrapper utility for cwl-runner or cwl-tools (CWL-based approach). Second, one can run workflows using CWL’s command-line and workflow instructions from within R (R-based approach). In the latter case the same CWL workflow definition files (e.g. *.cwl and *.yml) are used but rendered and executed entirely with R functions defined by systemPipeR, and thus use CWL mainly as a command-line and workflow definition format rather than execution software to run workflows. In this regard systemPipeR also provides several convenience functions that are useful for designing and debugging workflows, such as a command-line rendering function to retrieve the exact command-line strings for each data set and processing step prior to running a command-line.

Workflow Management with SYSargsList

The SYSargsList S4 class is a list-like container that stores the paths to all input and output files along with the corresponding parameters used in each analysis step (see Figure ??). SYSargsList instances are constructed from an optional targets files, and two CWL parameter files including *.cwl and *.yml (for details, see below). When running preconfigured NGS workflows, the only input the user needs to provide is the initial targets file containing the paths to the input files (e.g., FASTQ) and experiment design information, such as sample labels and biological replicates. Subsequent targets instances are created automatically, based on the connectivity establish between each workflow step. SYSargsList containers store all information required for one or multiple steps. This establishes central control for running, monitoring and debugging complex workflows from start to finish.

Workflow steps with input/output file operations are controlled by the SYSargsList container. Each of its components (SYSargs2) are constructed from an optional targets and two param files. Alternatively, LineWise instances containing pure R code can be used.

Command-line software support

systemPipeR adopted the widely used community standard Common Workflow Language (CWL) (Amstutz et al. 2016) for describing command-line tools and workflows in a declarative, generic, and reproducible manner. CWL specifications are text-based files and can be structured using YAML (https://yaml.org/) syntax. Therefore, the description files can be easily accessed and are readable. The significant advantage of adopting CWL as a standard description of command-line tools within is the flexibility of workflow reusability for different computing environments and workflow frameworks in the community, improving reproducibility, portability, and shareability between collaborators and community.

Following the CWL Command Line Tool Description Specification (https://www.commonwl.org/v1.2/CommandLineTool.html), the basic elements of the CWL tool description are defined in two files. Figure 3A-B illustrate the “hello world” example. The main file contains all the information necessary to build the command-line that will be executed, specifying the input, expected output files, and arguments for the command-line (Figure 3A). The second file is optional yet provides flexibility to assign values to parameters required to make the input or output objects when building the command-line.

Example of 'Hello World' message using CWL syntax and demonstrating the connectivity with `systemPipeR`. (A) This file describes the command-line tool, here using 'echo' command. (B) This file describes all the parameters variables connected with the tool specification file. Here the reference value of the input parameter can be specific or can be filled dynamically, adding a variable that connects with the targets files from `systemPipeR`. (C) `SYSargsList` function provides the 'inputvars' arguments to build the connectivity between the CWL description of parameters and the targets files. The argument requires a named vector where each vector element is required to be defined in the CWL description of parameters file (B), and the names of the elements are needed to match the column names defined in the targets file (D).

Figure 3: Example of ‘Hello World’ message using CWL syntax and demonstrating the connectivity with `systemPipeR`. (A) This file describes the command-line tool, here using ‘echo’ command. (B) This file describes all the parameters variables connected with the tool specification file. Here the reference value of the input parameter can be specific or can be filled dynamically, adding a variable that connects with the targets files from `systemPipeR`. (C) `SYSargsList` function provides the ‘inputvars’ arguments to build the connectivity between the CWL description of parameters and the targets files. The argument requires a named vector where each vector element is required to be defined in the CWL description of parameters file (B), and the names of the elements are needed to match the column names defined in the targets file (D).

Reference

Amstutz, Peter, Michael R Crusoe, Nebojša Tijanić, Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, et al. 2016. “Common Workflow Language, V1.0,” July. https://doi.org/10.6084/m9.figshare.3115156.v2.

H Backman, Tyler W, and Thomas Girke. 2016. “systemPipeR: NGS workflow and report generation environment.” BMC Bioinformatics 17 (1): 388. https://doi.org/10.1186/s12859-016-1241-0.

Last modified 2022-06-06: no_render (f8997482)