An R interface to the Common Workflow Language

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Documentation for package ‘Rcwl’ version 1.25.0

• 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