Define an Executable Pipeline Stage — pipeline

Defines one executable and its argument vector without invoking a shell. Stages can reference executables bundled by RBCFTools, executables exported by another package, or programs available on PATH.

Usage

pipeline_stage(command, args = character(), name = NULL)

Arguments

command: A length-one character string naming an executable or giving its path.
args: A character vector of arguments passed directly to the executable.
name: A label used in pipeline results. Defaults to the executable's basename.

Value

An object of class rbcftools_pipeline_stage.

Examples

pipeline_stage(samtools_path(), c("view", "--help"))
#> $command
#> [1] "/home/runner/work/_temp/Library/RBCFTools/samtools/bin/samtools"
#> 
#> $args
#> [1] "view"   "--help"
#> 
#> $name
#> [1] "samtools"
#> 
#> attr(,"class")
#> [1] "rbcftools_pipeline_stage"