R: Constructs SYSargs2 object from CWL param and targets files

loadWorkflow {systemPipeR}

R Documentation

Constructs SYSargs2 object from CWL param and targets files

Description

The constructor functions create an SYSargs2 S4 class object from three input files: a CWL param and input files, and one simple tabular files, a targets file. The latter is optional for workflow steps lacking input files. TheCWL param provides all the parameters required for running command-line software, following the standard and specification defined on Common Workflow Language (CWL). The input file provides additional information for the command-line, allowing each sample level input/outfile operation uses its own SYSargs2 instance. In the targets file users could provide the paths to the initial sample input files (e.g. FASTQ) along with sample labels, and if appropriate biological replicate and contrast information for controlling differential abundance analyses.

Usage

loadWorkflow(targets = NULL, wf_file, input_file, dir_path = ".")

Arguments

`targets`	path to `targets` file. Assign `NULL` to run the pipeline without 'targets' file. This can be useful for running specific workflows which do not require input files.
`wf_file`	path to `CWL param` file.
`input_file`	path to `input` file.
`dir_path`	full path to the directory with the `CWL param` and `input` files.

Details

Please note that the CWL param and input files need to be in the same directory.

Value

SYSargs2 object

Author(s)

Daniela Cassol and Thomas Girke

Examples

## Construct SYSargs2 object from CWl param, CWL input, and targets files 
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl", package="systemPipeR")
WF <- loadWorkflow(targets=targets, wf_file="hisat2-se/hisat2-mapping-se.cwl",
                   input_file="hisat2-se/hisat2-mapping-se.yml",
                   dir_path=dir_path)
WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH_", SampleName="_SampleName_"))
WF

[Package systemPipeR version 1.18.2 Index]