Edit workflow targets and modules — moduleReplace • metaboWorkflows

Edit the targets of a workflow definition.

Usage

moduleReplace(x, module, replacement)

# S4 method for Workflow
moduleReplace(x, module, replacement)

modulesRemove(x, modules)

# S4 method for Workflow
modulesRemove(x, modules)

modulesKeep(x, modules)

# S4 method for Workflow
modulesKeep(x, modules)

moduleAdd(x, module, addition)

# S4 method for Workflow
moduleAdd(x, module, addition)

targetReplace(x, module, target, replacement)

# S4 method for Workflow
targetReplace(x, module, target, replacement)

targetRemove(x, module, target)

# S4 method for Workflow
targetRemove(x, module, target)

targetAdd(x, module, target, addition)

# S4 method for Workflow
targetAdd(x, module, target, addition)

Arguments

x: S4 object of class Workflow
module: the workflow module name
replacement: the replacement workflow module or target
modules: character vector of module names
addition: the workflow module or target to add
target: the workflow target name

Value

S4 object of class Workflow with edited targets

Examples

## Define a workflow
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')
                                     
## Add a module
workflow_definition <- moduleAdd(workflow_definition,
                                 'additional_module',
                                 list(new_target = target('new_target','1 + 1')))
## Replace the additional module
workflow_definition <- moduleReplace(workflow_definition,
                                     'additional_module',
                                     list(replacement_target = target('replacement_target',
                                     '1 + 2')))
## Remove the additional module
workflow_definition <- modulesRemove(workflow_definition,
                                    'additional_module')

## Add a target to the input module
workflow_definition <- targetAdd(workflow_definition,
                                 'input',
                                 'new_target',
                                 target('new_target','1 + 1'))
## Replace the additional target
workflow_definition <- targetReplace(workflow_definition,
                                 'input',
                                 'new_target',
                                 target('new_target','1 + 2')) 
## Remove the additional target
workflow_definition <- targetRemove(workflow_definition,
                                 'input',
                                 'new_target')