An R interface to the Common Workflow Language


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Documentation for package ‘Rcwl’ version 1.6.0

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$-method Input parameters InputParam
$<--method Input parameters InputParam
+-method Pipeline
arguments cwlParam methods
arguments<- cwlParam methods
baseCommand cwlParam methods
baseCommand<- cwlParam methods
cwlClass cwlParam methods
cwlClass<- cwlParam methods
cwlParam Parameters for CWL
cwlParam-class Parameters for CWL
cwlShiny cwlShiny
cwlStepParam cwlStepParam
cwlStepParam-class cwlStepParam
cwlVersion cwlParam methods
cwlVersion<- cwlParam methods
Dirent requireDocker
extensions cwlParam methods
extensions<- cwlParam methods
hints cwlParam methods
hints<- cwlParam methods
InputArrayParam InputArrayParam
InputArrayParam-class InputArrayParam
InputParam Input parameters InputParam
InputParam-class Input parameters InputParam
InputParamList InputParamList
InputParamList-class InputParamList
inputs InputParamList
OutputArrayParam Output array parameters
OutputArrayParam-class Output array parameters
OutputParam Output parameters
OutputParam-class Output parameters
OutputParamList OutputParamList
OutputParamList-class OutputParamList
outputs OutputParamList
plotCWL plotCWL
Rcwl Rcwl
readCWL Read CWL Function to read CWL command or workflow files.
requireDocker requireDocker
requireInitialWorkDir requireDocker
requireJS requireDocker
requireManifest requireDocker
requirements cwlParam methods
requirements<- cwlParam methods
requireMultipleInput requireDocker
requireScatter requireDocker
requireSoftware requireDocker
requireStepInputExpression requireDocker
requireSubworkflow requireDocker
runCWL run cwlParam
runCWLBatch run CWL with batchtools
runs runs
short short
stdOut cwlParam methods
stdOut<- cwlParam methods
Step Step function
stepInParam stepInParam
stepInParam-class stepInParam
stepInParamList stepInParamList
stepInParamList-class stepInParamList
stepParam stepParam
stepParam-class stepParam
stepParamList stepParamList
stepParamList-class stepParamList
steps Steps
steps<- Steps
writeCWL Write CWL