systemPipeR 2.13.0
This is a Generic workflow template for building new workflows. It is provided by
systemPipeRdata,
a companion package to systemPipeR (H Backman and Girke 2016).
Similar to other systemPipeR workflow templates, a single command generates
the necessary working environment. This includes the expected directory structure
for executing systemPipeR workflows and parameter files for running
command-line (CL) software utilized in specific analysis steps.
In-depth information can be found in the main vignette of systemPipeRdata.
The Generic template presented here is special that it provides a workflow
skelleton intended to be used as a starting point for building new workflows.
Basic workflow steps are included to illustrate how to design command-line (CL)
and R-based workflow steps, as well as R Markdown code chunks that are not part
of a workflow. For more comprehensive information on designing
and executing workflows, users want to refer to the main vignettes of
systemPipeR
and
systemPipeRdata.
The details about contructing workflow steps are explained in the
Detailed Tutorial section
of systemPipeR's main vignette that uses the same workflow steps as the Generic workflow template.
The Rmd file (new.Rmd) associated with this vignette serves a dual purpose.
It acts both as a template for executing the workflow and as a template for
generating a reproducible scientific analysis report. Thus, users want to
customize the text (and/or code) of this or other systemPipeR workflow vignettes to describe their
experimental design and analysis results. This typically involves deleting the
instructions how to work with this workflow, and customizing the text
describing experimental designs, other metadata and analysis results.
The Generic workflow template includes the following four data processing steps.
The topology graph of this workflow template is shown in Figure 1.