Get and set methods for the Workflow S4 class.
Usage
# S4 method for Workflow
type(x)
# S4 method for Workflow
type(x) <- value
input(x)
# S4 method for Workflow
input(x)
input(x) <- value
# S4 method for Workflow
input(x) <- value
targets(x)
# S4 method for Workflow
targets(x)
targets(x) <- value
# S4 method for Workflow
targets(x) <- value
modules(x)
# S4 method for Workflow
modules(x)
# S4 method for Workflow
filePaths(x)
# S4 method for Workflow
filePaths(x) <- value
# S4 method for Workflow
sampleInformation(x)
# S4 method for Workflow
sampleInformation(x) <- value
# S4 method for Workflow
instrument(x)
# S4 method for Workflow
instrument(x) <- value
# S4 method for Workflow
directory(x)
# S4 method for Workflow
directory(x) <- value
# S4 method for Workflow
host(x)
# S4 method for Workflow
host(x) <- value
# S4 method for Workflow
port(x)
# S4 method for Workflow
port(x) <- value
# S4 method for Workflow
auth(x)
# S4 method for Workflow
auth(x) <- valueExamples
## Define a workflow with file path input
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')
## Return the workflow type
type(workflow_definition)
#> [1] "FIE-HRMS fingerprinting"
## Set the workflow type
type(workflow_definition) <- "RP-LC-HRMS profiling"
## Return the workflow input
input(workflow_definition)
#> File path workflow input
#> # files: 68
## Set the workflow input
if (FALSE) {
input(workflow_definition) <- inputGrover(instrument = 'An_instrument',
directory = 'Experiment_directory',
host = 'a.grover.host',
port = 80,
auth = '1234')
}
## Return the workflow targets for the input module
targets(workflow_definition)$input
#> $file_paths_list
#> ## Retrieve data file paths
#> tarchetypes::tar_file(
#> file_paths_list,
#> "data/file_paths.txt"
#> )
#>
#> $mzML
#> ## Track individual data files
#> hrmtargets::tar_export(
#> mzML,
#> readLines(file_paths_list)
#> )
#>
#> $sample_information_file
#> ## Sample information file path
#> tarchetypes::tar_file(
#> sample_information_file,
#> "data/runinfo.csv"
#> )
#>
#> $sample_information
#> ## Parse sample information
#> tar_target(
#> sample_information,
#> readr::read_csv(sample_information_file)
#> )
#>
## Set the workflow targets
targets(workflow_definition) <- list(
a_module = list(
a_target = target('a_target',
1 + 1,
args = list(memory = 'persistent'),
comment = 'A target')
)
)
## Return the workflow modules
modules(workflow_definition)
#> [1] "a_module"
## Return the workflow file paths
if (FALSE) {
filePaths(workflow_definition)
}
## Set the workflow file paths
filePaths(workflow_definition) <- 'a_file.mzML'
## Return the workflow sample information
sampleInformation(workflow_definition)
#> # A tibble: 68 × 7
#> fileOrder injOrder fileName batch block name class
#> <dbl> <dbl> <chr> <dbl> <dbl> <chr> <chr>
#> 1 1 64 1.mzML.gz 1 5 ABR1_1 ABR1
#> 2 2 40 10.mzML.gz 1 3 ABR1_10 ABR1
#> 3 3 52 11.mzML.gz 1 4 ABR1_11 ABR1
#> 4 4 67 12.mzML.gz 1 5 ABR1_12 ABR1
#> 5 5 32 13.mzML.gz 1 3 ABR1_13 ABR1
#> 6 6 53 14.mzML.gz 1 4 ABR1_14 ABR1
#> 7 7 4 15.mzML.gz 1 1 ABR1_15 ABR1
#> 8 8 34 16.mzML.gz 1 3 ABR5_1 ABR5
#> 9 9 38 17.mzML.gz 1 3 ABR5_2 ABR5
#> 10 10 59 18.mzML.gz 1 5 ABR5_3 ABR5
#> # ℹ 58 more rows
## Set the workflow sample information
sampleInformation(workflow_definition) <- tibble::tibble(fileName = 'a_file.mzML')
## Define a workflow with grover input
workflow_input <- inputGrover(instrument = 'An_instrument',
directory = 'Experiment_directory',
host = 'a.grover.host',
port = 80,
auth = '1234')
workflow_definition <- defineWorkflow(workflow_input,
'FIE-HRMS fingerprinting',
'Example project')
## Return the workflow instrument
instrument(workflow_definition)
#> [1] "An_instrument"
## Set the workflow Instrument
instrument(workflow_definition) <- 'A_different_instrument'
## Return the workflow directory
directory(workflow_definition)
#> [1] "Experiment_directory"
## Set the workflow directory
directory(workflow_definition) <- 'Another_experiment'
## Return the workflow host
host(workflow_definition)
#> [1] "a.grover.host"
## Set the workflow_host
host(workflow_definition) <- 'a.new.host'
## Return the workflow port
port(workflow_definition)
#> [1] 80
## Set the workflow port
port(workflow_definition) <- 81
## Return the workflow auth
auth(workflow_definition)
#> [1] "1234"
## Set the workflow auth
auth(workflow_definition) <- 'abcd'