nextflow.script
The nextflow.script
package implements the parsing and execution of Nextflow scripts.
Class Diagram
classDiagram
%%
%% nextflow.script
%%
CmdRun --> ScriptRunner : run
class ScriptRunner {
scriptFile : ScriptFile
session : Session
}
ScriptRunner --* ScriptFile
ScriptRunner --> ScriptParser : execute
ScriptParser --> BaseScript : parse
class ScriptFile {
source : Path
main : Path
repository : String
revisionInfo : AssetManager.RevisionInfo
localPath : Path
projectName : String
}
class BaseScript {
meta : ScriptMeta
entryFlow : WorkflowDef
}
BaseScript --* ScriptBinding
BaseScript --* ScriptMeta
BaseScript --> IncludeDef : include
IncludeDef --> ScriptParser : load0
class ScriptBinding {
scriptPath : Path
args : List~String~
params : ParamsMap
configEnv : Map
entryName : String
}
class ScriptMeta {
scriptPath : Path
definitions : Map
imports : Map
module : boolean
}
ScriptMeta "1" --* "*" ComponentDef : definitions
ScriptMeta "1" --* "*" ComponentDef : imports
ComponentDef <|-- FunctionDef
ComponentDef <|-- ProcessDef
ComponentDef <|-- WorkflowDef
class FunctionDef {
target : Object
name : String
alias : String
}
class ProcessDef {
processName : String
simpleName : String
baseName : String
rawBody : Closure~BodyDef~
}
ProcessDef --* ProcessConfig
ProcessDef --* BodyDef
ProcessDef --* ChannelOut
class WorkflowDef {
name : String
body : BodyDef
declaredInputs : List~String~
declaredOutputs : List~String~
variableNames : Set~String~
}
WorkflowDef --* BodyDef
WorkflowDef --* WorkflowBinding
WorkflowDef --* ChannelOut
class ProcessConfig {
configProperties : Map
inputs : InputsList
outputs : OutputsList
}
ProcessConfig --* InputsList
ProcessConfig --* OutputsList
class BodyDef {
closure : Closure
source : String
type : ScriptType
isShell : boolean
}
class ChannelOut {
target : List~DataflowWriteChannel~
channels : Map
}
class WorkflowBinding {
vars : Map
}
class InputsList {
target : List~InParam~
}
InputsList "1" --* "*" InParam
class OutputsList {
target : List~OutParam~
}
OutputsList "1" --* "*" OutParam
%% InParam <|-- BaseInParam
%% BaseInParam <|-- EachInParam
%% BaseInParam <|-- EnvInParam
%% BaseInParam <|-- FileInParam
%% BaseInParam <|-- StdInParam
%% BaseInParam <|-- TupleInParam
%% BaseInParam <|-- ValueInParam
%% OutParam <|-- BaseOutParam
%% BaseOutParam <|-- EachOutParam
%% BaseOutParam <|-- EnvOutParam
%% BaseOutParam <|-- FileOutParam
%% BaseOutParam <|-- StdOutParam
%% BaseOutParam <|-- TupleOutParam
%% BaseOutParam <|-- ValueOutParam
Note
Some classes may be excluded from the above diagram for brevity.
Notes
The execution of a Nextflow pipeline occurs in two phases. In the first phase, Nextflow parses and runs the script (using the language extensions in nextflow.ast and nextflow.extension), which produces the workflow DAG. In the second phase, Nextflow executes the workflow.
Note
In DSL1, there was no separation between workflow construction and execution – dataflow operators were executed as soon as they were constructed. DSL2 introduced lazy execution in order to separate process definition from execution, and thereby facilitate subworkflows and modules.