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
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.
Object of class
variables list defined in the
Daniela Cassol and Thomas Girke
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## 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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