An R interface to the Common Workflow Language

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Documentation for package ‘Rcwl’ version 1.8.0

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Rcwl,Rcwl-package Rcwl-package
Rcwl-package Rcwl-package
$-method cwlProcess methods
$<--method cwlProcess methods
+-method cwlWorkflow function
arguments cwlProcess methods
arguments<- cwlProcess methods
baseCommand cwlProcess methods
baseCommand<- cwlProcess methods
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
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_udocker install udocker
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
requireInitialWorkDir CWL requirements functions
requireJS CWL requirements functions
requireManifest CWL requirements functions
requirements cwlProcess methods
requirements<- cwlProcess methods
requireMultipleInput CWL requirements functions
requireRscript CWL requirements functions
requireScatter CWL requirements functions
requireSoftware CWL requirements functions
requireStepInputExpression CWL requirements functions
requireSubworkflow CWL requirements functions
runCWL run cwlProcess
runCWLBatch run CWL with batchtools
runs cwlWorkflow methods
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.
steps cwlWorkflow function
steps<- cwlWorkflow function
writeCWL Write CWL