workflow-edit: Edit workflow targets and modules

In jasenfinch/metaboWorkflows: Workflow Project Templates for Metabolomics Analyses

Edit workflow targets and modules

Description

Edit the targets of a workflow definition.

Usage

moduleReplace(x, module, replacement)

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

modulesRemove(x, modules)

## S4 method for signature 'Workflow'
modulesRemove(x, modules)

modulesKeep(x, modules)

## S4 method for signature 'Workflow'
modulesKeep(x, modules)

moduleAdd(x, module, addition)

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

targetReplace(x, module, target, replacement)

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

targetRemove(x, module, target)

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

targetAdd(x, module, target, addition)

## S4 method for signature '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')

jasenfinch/metaboWorkflows documentation built on May 24, 2023, 8:23 a.m.