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Define a metabolomics workflow

Source: R/define.R
defineWorkflow.Rd

Define a metabolomics data analysis workflow for a given input type and workflow name.

Usage

defineWorkflow(input, workflow, project_name, ...)

# S4 method for GroverInput
defineWorkflow(input, workflow, project_name, ...)

# S4 method for FilePathInput
defineWorkflow(input, workflow, project_name, ...)

Arguments

input

S4 object of class GroverInput or FilePathInput

workflow

workflow name as returned by availableWorkflows()

project_name

the project name

...

arguments to pass to defineProject. See details.

Value

An S4 object of class Workflow

Details

Further project template options such as the use of the R package renv for R package management can also be declared, which are passed to defineProject(). See the defineProject() documentation for details on these options.

See also

defineProject()

Examples

file_paths <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')
sample_information <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')

workflow_input <- inputFilePath(file_paths,sample_information)

workflow_definition <- defineWorkflow(workflow_input,
                                      'FIE-HRMS fingerprinting',
                                      'Example project')
workflow_definition
#> Workflow:  FIE-HRMS fingerprinting 
#> 
#> Project name: Example project 
#> Directory path: . 
#> Use renv: TRUE 
#> Docker: TRUE 
#> GitHub repository: FALSE 
#> Private repository: FALSE 
#> GitHub Actions: FALSE 
#> Parallel plan: jfmisc::suitableParallelPlan() 
#> Force creation: FALSE 
#> 
#> File path workflow input
#> # files: 68
#> 
#> # targets: 37