# An R interface to the Common Workflow Language

## Documentation for package ‘Rcwl’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

Rcwl,Rcwl-package | Rcwl-package
Rcwl-package | Rcwl-package
$-method | cwlProcess methods
$<--method | cwlProcess methods
+-method | cwlWorkflow function
addMeta | addMeta Add or change meta information for a cwl recipe.
arguments | cwlProcess methods
arguments<- | cwlProcess methods
baseCommand | cwlProcess methods
baseCommand<- | cwlProcess methods
condaPackage | CWL requirements functions
CondaTool | CWL requirements functions
cwl-requirements | CWL requirements functions
cwlClass | cwlProcess methods
cwlClass<- | cwlProcess methods
cwlProcess | Parameters for CWL
cwlProcess-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
cwlProcess-methods | cwlProcess methods
cwlShiny | cwlShiny
cwlStep | cwlStep function
cwlStep-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
cwlStepList | All classes defined in the package of 'Rcwl' and the class constructor functions.
cwlStepList-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
cwlVersion | cwlProcess methods
cwlVersion<- | cwlProcess methods
cwlWorkflow | cwlWorkflow function
cwlWorkflow-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
cwlWorkflow-methods | cwlWorkflow methods
Dirent | CWL requirements functions
env_Rcwl | Rcwl conda environment
extensions | cwlProcess methods
extensions<- | cwlProcess methods
hints | cwlProcess methods
hints<- | cwlProcess methods
InputArrayParam | All classes defined in the package of 'Rcwl' and the class constructor functions.
InputArrayParam-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
InputParam | All classes defined in the package of 'Rcwl' and the class constructor functions.
InputParam-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
InputParamList | All classes defined in the package of 'Rcwl' and the class constructor functions.
InputParamList-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
inputs | cwlProcess methods
install_cwltool | install cwltool
install_udocker | install udocker
meta | addMeta Add or change meta information for a cwl recipe.
meta<- | addMeta Add or change meta information for a cwl recipe.
OutputArrayParam | All classes defined in the package of 'Rcwl' and the class constructor functions.
OutputArrayParam-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
OutputParam | All classes defined in the package of 'Rcwl' and the class constructor functions.
OutputParam-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
OutputParamList | All classes defined in the package of 'Rcwl' and the class constructor functions.
OutputParamList-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
outputs | cwlProcess methods
plotCWL | plotCWL
Rcwl | Rcwl-package
readCWL | Read CWL Function to read CWL command or workflow files.
requireDocker | CWL requirements functions
requireEnvVar | CWL requirements functions
requireInitialWorkDir | CWL requirements functions
requireJS | CWL requirements functions
requireManifest | CWL requirements functions
requirements | cwlProcess methods
requirements<- | cwlProcess methods
requireMultipleInput | CWL requirements functions
requireNetwork | CWL requirements functions
requireResource | CWL requirements functions
requireRscript | CWL requirements functions
requireScatter | CWL requirements functions
requireShellCommand | CWL requirements functions
requireShellScript | CWL requirements functions
requireSoftware | CWL requirements functions
requireStepInputExpression | CWL requirements functions
requireSubworkflow | CWL requirements functions
runCWL | run cwlProcess
runCWLBatch | run CWL with batchtools
runCWLBP | run CWL with BiocParallel
runs | cwlWorkflow methods
ShellScript | CWL requirements functions
short | cwlProcess methods
stdOut | cwlProcess methods
stdOut<- | cwlProcess methods
stepInParam | All classes defined in the package of 'Rcwl' and the class constructor functions.
stepInParam-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
stepInParamList | All classes defined in the package of 'Rcwl' and the class constructor functions.
stepInParamList-class | All classes defined in the package of 'Rcwl' and the class constructor functions.
stepInputs | stepInputs
stepOutputs | stepOutputs
steps | cwlWorkflow function
steps<- | cwlWorkflow function
writeCWL | Write CWL