Description Usage Arguments Value Author(s) See Also Examples
The SYSargs2
S4 class object is constructed from the loadWorkflow
, which 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. The renderWF
function populates all the command-line for each sample in each step of the particular workflow. Each sample level input/outfile operation uses its own SYSargs2
instance. The output of SYSargs2
define all the expected output files for each step in the workflow, which usually it is the sample input for the next step in an SYSargs2
instance. Between different instances, this connectivity is established by writing the subsetting output with the writeTargetsout
function to a new targets file that serves as input to the next loadWorkflow
and renderWF
call. By chaining several SYSargs2
steps together one can construct complex workflows involving many sample-level input/output file operations with any combination of command-line or R-based software.
1 |
WF |
Object of class |
inputvars |
variables list defined in the |
SYSargs2
object
Daniela Cassol and Thomas Girke
showClass("SYSargs2")
loadWorkflow
writeTargetsout
1 2 3 4 5 6 7 | ## 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/hisat2/hisat2-se", package="systemPipeR")
WF <- loadWorkflow(targets=targets, wf_file="hisat2-mapping-se.cwl",
input_file="hisat2-mapping-se.yml", dir_path=dir_path)
WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
WF
|
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