SYSargs2Pipe-class {systemPipeR} | R Documentation |
"SYSargs2Pipe"
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 can be created by calls of the form new("SYSargs2Pipe", ...)
.
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
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
signature(from = "list", to = "SYSargs2Pipe")
: as(list, "SYSargs2Pipe")
signature(from = "SYSargs2Pipe", to = "list")
: as(SYSargs2Pipe, "list")
signature(x = "SYSargs2Pipe")
: extracts number of SYSargs2
objects
signature(x = "SYSargs2Pipe")
: extracts slot names
signature(object = "SYSargs2Pipe")
: summary view of SYSargs2
objects
signature(x = "SYSargs2Pipe")
: extract data from targets
slot
signature(x = "SYSargs2Pipe")
: Coerce back to list as(SYSargs2Pipe, "list")
signature(x = "SYSargs2Pipe")
: extract data from track
slot
signature(x = "SYSargs2Pipe")
: extract data from WF_steps
slot
Daniela Cassol and Thomas Girke
loadWorkflow
and renderWF
and runCommandline
and clusterRun
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]