CmdRun (nextflow 0.25.0 API)

nextflow.cli.CmdRun

All Implemented Interfaces and Traits:: HubOptions

@groovy.util.logging.Slf4j
@groovy.transform.CompileStatic
@com.beust.jcommander.Parameters(commandDescription = "Execute a pipeline project")
class CmdRun
extends CmdBase

CLI sub-command RUN

Authors:: Paolo Di Tommaso

Nested Class Summary

Nested classes
Modifiers	Name	Description
`static class`	`CmdRun.DurationConverter`

Field Summary

Fields
Modifiers	Name	Description
`static java.lang.Object`	`NAME`

Properties Summary

Properties
Type	Name and description
`static java.util.List<java.lang.String>`	`VALID_PARAMS_FILE`
`java.util.List<java.lang.String>`	`args`
`boolean`	`cacheable`
`java.util.Map<java.lang.String, java.lang.String>`	`clusterOptions`
`boolean`	`dumpHashes`
`java.util.Map<java.lang.String, java.lang.String>`	`env`
`java.util.Map<java.lang.String, java.lang.String>`	`executorOptions`
`boolean`	`exportSysEnv`
`boolean`	`latest`
`java.lang.String`	`libPath`
`java.util.Map<java.lang.String, java.lang.String>`	`params` Defines the parameters to be passed to the pipeline script
`java.lang.String`	`paramsFile`
`long`	`pollInterval`
`java.lang.Integer`	`poolSize`
`java.util.Map<java.lang.String, java.lang.String>`	`process`
`java.lang.String`	`profile`
`java.lang.Integer`	`queueSize`
`java.lang.String`	`resume`
`java.lang.String`	`revision`
`java.util.List<java.lang.String>`	`runConfig`
`java.lang.String`	`runName`
`boolean`	`stdin`
`java.lang.String`	`test`
`java.lang.String`	`withDag`
`java.lang.Object`	`withDocker`
`java.lang.String`	`withDrmaa`
`boolean`	`withExtrae`
`boolean`	`withMpi`
`java.lang.Object`	`withSingularity`
`java.lang.String`	`withTimeline`
`java.lang.String`	`withTrace`
`boolean`	`withoutDocker`
`java.lang.String`	`workDir`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`java.lang.String`	`getName()`
	`java.util.Map`	`getParsedParams()`
	`protected ScriptFile`	`getScriptFile(java.lang.String pipelineName)`
	`protected static java.io.File`	`getScriptFromStream(java.io.InputStream input, java.lang.String name = 'nextflow' )`
	`void`	`run()`
	`void`	`setBackground(boolean value)`
	`protected static java.io.File`	`tryReadFromStdin()`

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class CmdBase`	`getLauncher, getName, setLauncher`
`class java.lang.Object`	`java.lang.Object#wait(long, int), java.lang.Object#wait(long), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll()`

- Field Detail
  - public static final java.lang.Object NAME
- Property Detail
  - static java.util.List<java.lang.String> VALID_PARAMS_FILE
  - @com.beust.jcommander.Parameter(description = 'project name or repository url') java.util.List<java.lang.String> args
  - @com.beust.jcommander.Parameter(names=['-cache'], description = 'enable/disable processes caching', arity = 1) boolean cacheable
  - @com.beust.jcommander.DynamicParameter(names = ['-cluster.'], description = 'Define cluster options', hidden = true ) java.util.Map<java.lang.String, java.lang.String> clusterOptions
  - @com.beust.jcommander.Parameter(names=['-dump-hashes'], description = 'Dump task hash keys for debugging purpose') boolean dumpHashes
  - @com.beust.jcommander.DynamicParameter(names = ['-e.'], description = 'Add the specified variable to execution environment') java.util.Map<java.lang.String, java.lang.String> env
  - @com.beust.jcommander.DynamicParameter(names = ['-executor.'], description = 'Executor(s) options', hidden = true ) java.util.Map<java.lang.String, java.lang.String> executorOptions
  - @com.beust.jcommander.Parameter(names = ['-E'], description = 'Exports all the current system environment') boolean exportSysEnv
  - @com.beust.jcommander.Parameter(names=['-latest'], description = 'Pull latest changes before run') boolean latest
  - @com.beust.jcommander.Parameter(names=['-lib'], description = 'Library extension path') java.lang.String libPath
  - @com.beust.jcommander.DynamicParameter(names = '--', description = 'Set a parameter used by the pipeline', hidden = true) java.util.Map<java.lang.String, java.lang.String> params
    
    Defines the parameters to be passed to the pipeline script
  - @com.beust.jcommander.Parameter(names='-params-file', description = 'Load script parameters from a JSON/YAML file') java.lang.String paramsFile
  - @com.beust.jcommander.Parameter(names=['-pi','-poll-interval'], description = 'Executor poll interval (duration string ending with ms|s|m)', converter = DurationConverter, hidden = true) long pollInterval
  - @com.beust.jcommander.Parameter(names=['-ps','-pool-size'], description = 'Number of threads in the execution pool', hidden = true) java.lang.Integer poolSize
  - @com.beust.jcommander.DynamicParameter(names = ['-process.'], description = 'Set process default options' ) java.util.Map<java.lang.String, java.lang.String> process
  - @com.beust.jcommander.Parameter(names=['-profile'], description = 'Choose a configuration profile') java.lang.String profile
  - @com.beust.jcommander.Parameter(names=['-qs','-queue-size'], description = 'Max number of processes that can be executed in parallel by each executor') java.lang.Integer queueSize
  - @com.beust.jcommander.Parameter(names=['-resume'], description = 'Execute the script using the cached results, useful to continue executions that was stopped by an error') java.lang.String resume
  - @com.beust.jcommander.Parameter(names=['-r','-revision'], description = 'Revision of the project to run (either a git branch, tag or commit SHA number)') java.lang.String revision
  - @com.beust.jcommander.Parameter(names=['-c','-config'], hidden = true ) java.util.List<java.lang.String> runConfig
  - @com.beust.jcommander.Parameter(names=['-name'], description = 'Assign a mnemonic name to the a pipeline run') java.lang.String runName
  - @com.beust.jcommander.Parameter(names='-stdin', hidden = true) boolean stdin
  - @com.beust.jcommander.Parameter(names=['-test'], description = 'Test function with the specified name') java.lang.String test
  - @com.beust.jcommander.Parameter(names = '-with-dag', description = 'Create pipeline DAG file') java.lang.String withDag
  - @com.beust.jcommander.Parameter(names = '-with-docker', description = 'Enable process execution in a Docker container') java.lang.Object withDocker
  - @com.beust.jcommander.Parameter(names = ['-with-drmaa'], description = 'Enable DRMAA binding') java.lang.String withDrmaa
  - @com.beust.jcommander.Parameter(names = ['-with-extrae'], description = 'Trace execution by using BSC Extrae', arity = 0, hidden = true) boolean withExtrae
  - @com.beust.jcommander.Parameter(names = '-with-mpi', hidden = true) boolean withMpi
  - @com.beust.jcommander.Parameter(names = '-with-singularity', description = 'Enable process execution in a Singularity container') java.lang.Object withSingularity
  - @com.beust.jcommander.Parameter(names = ['-with-timeline'], description = 'Create processes execution timeline file') java.lang.String withTimeline
  - @com.beust.jcommander.Parameter(names = ['-with-trace'], description = 'Create processes execution tracing file') java.lang.String withTrace
  - @com.beust.jcommander.Parameter(names = '-without-docker', description = 'Disable process execution with Docker', arity = 0) boolean withoutDocker
  - @com.beust.jcommander.Parameter(names=['-w', '-work-dir'], description = 'Directory where intermediate results are stored') java.lang.String workDir
- Method Detail
  - @java.lang.Override final java.lang.String getName()
  - java.util.Map getParsedParams()
  - protected ScriptFile getScriptFile(java.lang.String pipelineName)
  - protected static java.io.File getScriptFromStream(java.io.InputStream input, java.lang.String name = 'nextflow' )
  - @java.lang.Override void run()
  - @com.beust.jcommander.Parameter(names = ['-bg'], arity = 0, hidden = true) void setBackground(boolean value)
  - protected static java.io.File tryReadFromStdin()

Summary:
Nested
Field
Property
Method

| Detail:
Field
Property
Method

Groovy Documentation

[Groovy] Class CmdRun

Nested Class Summary

Field Summary

Properties Summary

Methods Summary

Inherited Methods Summary

Field Detail

public static final java.lang.Object NAME

Property Detail

static java.util.List<java.lang.String> VALID_PARAMS_FILE

@com.beust.jcommander.Parameter(description = 'project name or repository url') java.util.List<java.lang.String> args

@com.beust.jcommander.Parameter(names=['-cache'], description = 'enable/disable processes caching', arity = 1) boolean cacheable

@com.beust.jcommander.DynamicParameter(names = ['-cluster.'], description = 'Define cluster options', hidden = true ) java.util.Map<java.lang.String, java.lang.String> clusterOptions

@com.beust.jcommander.Parameter(names=['-dump-hashes'], description = 'Dump task hash keys for debugging purpose') boolean dumpHashes

@com.beust.jcommander.DynamicParameter(names = ['-e.'], description = 'Add the specified variable to execution environment') java.util.Map<java.lang.String, java.lang.String> env

@com.beust.jcommander.DynamicParameter(names = ['-executor.'], description = 'Executor(s) options', hidden = true ) java.util.Map<java.lang.String, java.lang.String> executorOptions

@com.beust.jcommander.Parameter(names = ['-E'], description = 'Exports all the current system environment') boolean exportSysEnv

@com.beust.jcommander.Parameter(names=['-latest'], description = 'Pull latest changes before run') boolean latest

@com.beust.jcommander.Parameter(names=['-lib'], description = 'Library extension path') java.lang.String libPath

@com.beust.jcommander.DynamicParameter(names = '--', description = 'Set a parameter used by the pipeline', hidden = true) java.util.Map<java.lang.String, java.lang.String> params

@com.beust.jcommander.Parameter(names='-params-file', description = 'Load script parameters from a JSON/YAML file') java.lang.String paramsFile

@com.beust.jcommander.Parameter(names=['-pi','-poll-interval'], description = 'Executor poll interval (duration string ending with ms|s|m)', converter = DurationConverter, hidden = true) long pollInterval

@com.beust.jcommander.Parameter(names=['-ps','-pool-size'], description = 'Number of threads in the execution pool', hidden = true) java.lang.Integer poolSize

@com.beust.jcommander.DynamicParameter(names = ['-process.'], description = 'Set process default options' ) java.util.Map<java.lang.String, java.lang.String> process

@com.beust.jcommander.Parameter(names=['-profile'], description = 'Choose a configuration profile') java.lang.String profile

@com.beust.jcommander.Parameter(names=['-qs','-queue-size'], description = 'Max number of processes that can be executed in parallel by each executor') java.lang.Integer queueSize

@com.beust.jcommander.Parameter(names=['-resume'], description = 'Execute the script using the cached results, useful to continue executions that was stopped by an error') java.lang.String resume

@com.beust.jcommander.Parameter(names=['-r','-revision'], description = 'Revision of the project to run (either a git branch, tag or commit SHA number)') java.lang.String revision

@com.beust.jcommander.Parameter(names=['-c','-config'], hidden = true ) java.util.List<java.lang.String> runConfig

@com.beust.jcommander.Parameter(names=['-name'], description = 'Assign a mnemonic name to the a pipeline run') java.lang.String runName

@com.beust.jcommander.Parameter(names='-stdin', hidden = true) boolean stdin

@com.beust.jcommander.Parameter(names=['-test'], description = 'Test function with the specified name') java.lang.String test

@com.beust.jcommander.Parameter(names = '-with-dag', description = 'Create pipeline DAG file') java.lang.String withDag

@com.beust.jcommander.Parameter(names = '-with-docker', description = 'Enable process execution in a Docker container') java.lang.Object withDocker

@com.beust.jcommander.Parameter(names = ['-with-drmaa'], description = 'Enable DRMAA binding') java.lang.String withDrmaa

@com.beust.jcommander.Parameter(names = ['-with-extrae'], description = 'Trace execution by using BSC Extrae', arity = 0, hidden = true) boolean withExtrae

@com.beust.jcommander.Parameter(names = '-with-mpi', hidden = true) boolean withMpi

@com.beust.jcommander.Parameter(names = '-with-singularity', description = 'Enable process execution in a Singularity container') java.lang.Object withSingularity

@com.beust.jcommander.Parameter(names = ['-with-timeline'], description = 'Create processes execution timeline file') java.lang.String withTimeline

@com.beust.jcommander.Parameter(names = ['-with-trace'], description = 'Create processes execution tracing file') java.lang.String withTrace

@com.beust.jcommander.Parameter(names = '-without-docker', description = 'Disable process execution with Docker', arity = 0) boolean withoutDocker

@com.beust.jcommander.Parameter(names=['-w', '-work-dir'], description = 'Directory where intermediate results are stored') java.lang.String workDir

Method Detail

@java.lang.Override final java.lang.String getName()

java.util.Map getParsedParams()

protected ScriptFile getScriptFile(java.lang.String pipelineName)

protected static java.io.File getScriptFromStream(java.io.InputStream input, java.lang.String name = 'nextflow' )

@java.lang.Override void run()

@com.beust.jcommander.Parameter(names = ['-bg'], arity = 0, hidden = true) void setBackground(boolean value)

protected static java.io.File tryReadFromStdin()