The package MagellanNTK is a Shiny application which provides the infrastructure for the configuration, the execution and the surveillance of a defined sequence of computational tasks for data analysis, hereafter called “pipelines”. It builds graphical pipelines based on third party packages, developed as Shiny modules. It proposes a framework to navigate between steps of a complex data processing tool when the succession of processes is mostly chronological.
For example, if a process is composed of three steps, then it is very easy to run the first step, then the second and finally the last one. It is like a dataflow manager.
Moreover, this navigation system, which is at the core of MagellanNTK, can by used at several levels. It can then be possible to define, for example, a super-process (i.e. a pipeline) in which each step is a whole process containing itself several steps.
Installation
To install MagellanNTK:
{r install, eval = FALSE} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MagellanNTK")
Using MagellanNTK
Launching a pipeline
In the following example, the pipeline called PipelineDemo is launched.
library(MagellanNTK)
wf.path <- system.file('workflow/PipelineDemo', package = 'MagellanNTK')
MagellanNTK(wf.path, 'PipelineDemo')Launching a single process
In the following example, only the Preprocessing process is launched.
library(MagellanNTK)
wf.path <- system.file('workflow/PipelineDemo', package = 'MagellanNTK')
MagellanNTK(wf.path, 'PipelineDemo_Preprocessing')