SYSargs2Pipe-class {systemPipeR} | R Documentation

## Class `"SYSargs2Pipe"`

### Description

`SYSargs2Pipe class` stores a list `SYSargs2` objects. Each `SYSargs2` objects stores all the information and instructions needed for processing a set of input files with a specific command-line or a series of command-line within a workflow.

### Objects from the Class

Objects can be created by calls of the form `new("SYSargs2Pipe", ...)`.

### Slots

`WF_steps`:

  Object of class `"list"` storing all the `SYSargs2` objects

`track`:

  Object of class `"list"` storing all the output files from each `SYSargs2` objects

`summaryWF`:

  Object of class `"list"` storing the summary of all the expected files exists and how many were missing for each `SYSargs2` objects

### Methods

[

  `signature(x = "SYSargs2Pipe", i = "ANY", j = "ANY", drop = "ANY")`: subsetting of class with bracket operator

[[

  `signature(x = "SYSargs2Pipe", i = "ANY", j = "ANY")`: subsetting of class with bracket operator

[[<-

  `signature(x = "SYSargs2Pipe", i = "ANY", j = "ANY", value = "ANY")`: replacement method for SYSargs2 class

$

  `signature(x = "SYSargs2Pipe")`: extracting slots elements by name

coerce

  `signature(from = "list", to = "SYSargs2Pipe")`: `as(list, "SYSargs2Pipe")`

coerce

  `signature(from = "SYSargs2Pipe", to = "list")`: `as(SYSargs2Pipe, "list")`

length

  `signature(x = "SYSargs2Pipe")`: extracts number of `SYSargs2` objects

names

  `signature(x = "SYSargs2Pipe")`: extracts slot names

show

  `signature(object = "SYSargs2Pipe")`: summary view of `SYSargs2` objects

summaryWF

  `signature(x = "SYSargs2Pipe")`: extract data from `targets` slot

SYSargs2Pipe_ls

  `signature(x = "SYSargs2Pipe")`: Coerce back to list `as(SYSargs2Pipe, "list")`

track

  `signature(x = "SYSargs2Pipe")`: extract data from `track` slot

WF_steps

  `signature(x = "SYSargs2Pipe")`: extract data from `WF_steps` slot

### Author(s)

Daniela Cassol and Thomas Girke

### See Also

`loadWorkflow` and `renderWF` and `runCommandline` and `clusterRun`

### Examples

    showClass("SYSargs2Pipe")

    ## 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

    ## Keep track
    WF_set <- run_track(WF_ls = c(WF))
    WF_steps(WF_set)
    track(WF_set)
    summaryWF(WF_set)[1]

[Package systemPipeR version 1.18.2 Index]