ScriptRunner (nextflow 0.25.0 API)

nextflow.script.ScriptRunner

Application main class
Authors:
Paolo Di Tommaso

Nested Class Summary

Nested classes
Modifiers	Name	Description
`static class`	`ScriptRunner.ArgsList`	Extends an `ArrayList` class adding a nicer index-out-of-range error message

Properties Summary

Properties
Type	Name and description
`java.lang.String`	`profile` The used configuration profile

Constructor Summary

Constructors
Constructor and description
`ScriptRunner ()` Instantiate the runner object creating a new session
`ScriptRunner (java.util.Map config)`
`ScriptRunner (Session session)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`java.lang.Object`	`execute(java.util.List<java.lang.String> args = null )` Execute a Nextflow script, it does the following: parse the script launch script execution await for all tasks completion
	`protected java.lang.Object`	`fetchContainers()`
	`java.lang.Object`	`getResult()` @return The result produced by the script execution
	`BaseScript`	`getScriptObj()` @return The interpreted script object
	`Session`	`getSession()`
	`java.lang.Object`	`normalizeOutput()`
	`protected BaseScript`	`parseScript(java.io.File file, java.util.List<java.lang.String> args = null )`
	`protected BaseScript`	`parseScript(java.lang.String scriptText, java.util.List<java.lang.String> args = null)`
	`protected java.lang.Object`	`run()` Launch the Nextflow script execution
	`ScriptRunner`	`setScript(ScriptFile script)`
	`ScriptRunner`	`setScript(java.lang.String text)`
	`protected java.lang.Object`	`terminate()`
	`java.lang.Object`	`test(java.lang.String methodName, java.util.List<java.lang.String> args = null )` Test the name specified by the `methodName`
	`void`	`verifyAndTrackHistory(java.lang.String cli, java.lang.String name)` @param cli The launcher command line string

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`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()`

- Property Detail
  - java.lang.String profile
    
    The used configuration profile
- Constructor Detail
  - ScriptRunner()
    
    Instantiate the runner object creating a new session
  - ScriptRunner(java.util.Map config)
  - ScriptRunner(Session session)
- Method Detail
  - java.lang.Object execute(java.util.List<java.lang.String> args = null )
    
    Execute a Nextflow script, it does the following:
  - parse the script
  - launch script execution
  - await for all tasks completion
    Parameters:
    scriptFile - The file containing the script to be executed
    args - The arguments to be passed to the script
    Returns:
    The result as returned by the #run method
  - @groovy.transform.CompileDynamic protected java.lang.Object fetchContainers()
  - java.lang.Object getResult()
    
    Returns:
    The result produced by the script execution
  - BaseScript getScriptObj()
    
    Returns:
    The interpreted script object
  - Session getSession()
  - java.lang.Object normalizeOutput()
  - protected BaseScript parseScript(java.io.File file, java.util.List<java.lang.String> args = null )
  - protected BaseScript parseScript(java.lang.String scriptText, java.util.List<java.lang.String> args = null)
  - protected java.lang.Object run()
    
    Launch the Nextflow script execution
    Returns:
    The value as returned by the user provided script
  - ScriptRunner setScript(ScriptFile script)
  - ScriptRunner setScript(java.lang.String text)
  - protected java.lang.Object terminate()
  - java.lang.Object test(java.lang.String methodName, java.util.List<java.lang.String> args = null )
    
    Test the name specified by the methodName
    Parameters:
    scriptText
    methodName
    args
  - void verifyAndTrackHistory(java.lang.String cli, java.lang.String name)
    
    Parameters:
    cli - The launcher command line string

Summary:
Nested
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation

[Groovy] Class ScriptRunner

Nested Class Summary

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Property Detail

java.lang.String profile

Constructor Detail

ScriptRunner()

ScriptRunner(java.util.Map config)

ScriptRunner(Session session)

Method Detail

java.lang.Object execute(java.util.List<java.lang.String> args = null )

@groovy.transform.CompileDynamic protected java.lang.Object fetchContainers()

java.lang.Object getResult()

BaseScript getScriptObj()

Session getSession()

java.lang.Object normalizeOutput()

protected BaseScript parseScript(java.io.File file, java.util.List<java.lang.String> args = null )

protected BaseScript parseScript(java.lang.String scriptText, java.util.List<java.lang.String> args = null)

protected java.lang.Object run()

ScriptRunner setScript(ScriptFile script)

ScriptRunner setScript(java.lang.String text)

protected java.lang.Object terminate()

java.lang.Object test(java.lang.String methodName, java.util.List<java.lang.String> args = null )

void verifyAndTrackHistory(java.lang.String cli, java.lang.String name)