A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

abort(Throwable) - Method in Session

Terminate the pipeline execution killing all running tasks

AbortOperationException - Class in nextflow.exception

Abort the current operation execution

AbortRunException - Class in nextflow.exception

Exception thrown when execution is aborted by a failing process

AbortSignalException - Class in nextflow.exception

Adaptor exception to wrap a termination signal

AbortSignalException(Signal) - Constructor in AbortSignalException

AbstractBinarySplitter - Class in nextflow.splitter

Base class for splitter handling binary data

AbstractGridExecutor - Class in nextflow.executor

Generic task processor executing a task through a grid facility

AbstractGridExecutor.QueueStatus - Enum in nextflow.executor

Status as returned by the grid engine

AbstractSplitter - Class in nextflow.splitter

Generic data splitter, provide main methods/interfaces

AbstractSplitter(Map) - Constructor in AbstractSplitter

Create a splitter object with the specified option parameters

AbstractTextSplitter - Class in nextflow.splitter

Implements an abstract text splitting for the main types

add(Object) - Method in CharSequenceCollector

add(Object) - Method in CollectorStrategy

@param item Add an item to the current chunk

add(String, def) - Method in FileCollector

Add and entry to the collector set

add(Object) - Method in ObjectListCollector

add(String) - Method in PathTrie

Add a string path to the collection

add(String, def) - Method in SimpleFileCollector

add(String, def) - Method in SortFileCollector

Append a user value to the file collection

add(Object) - Method in TextFileCollector

addContainerRunCommand(ContainerScriptTokens) - Method in ContainerBuilder

Given a normalised shell script (starting with a she-bang line) replace the first token on the first line with a docker run command

addEngineOptions(String) - Method in ContainerBuilder

addEnv(def) - Method in ContainerBuilder

addMount(Path) - Method in ContainerBuilder

addMountForInputs(Map<String, Path>) - Method in ContainerBuilder

addOperatorNode(String, def, def, List<DataflowProcessor>) - Method in DAG

Creates a new DAG vertex representing a dataflow operator

addOperatorNode(String, def, def) - Method in NodeMarker

Creates a new DAG vertex representing a dataflow operator

addProcessNode(String, InputsList, OutputsList, TaskProcessor) - Method in DAG

Creates a new vertex in the DAG representing a computing `process`

addProcessNode(TaskProcessor, InputsList, OutputsList) - Method in NodeMarker

Creates a new vertex in the DAG representing a computing `process`

addRunOptions(String) - Method in ContainerBuilder

addRunOptions(String) - Method in SingularityBuilder

addSourceNode(String, def) - Method in DAG

Creates a vertex in the DAG representing a dataflow channel source.

addSourceNode(String, def) - Method in NodeMarker

Creates a vertex in the DAG representing a dataflow channel source.

addWhenGuardCall(List<Statement>, StringBuilder, BlockStatement) - Method in NextflowDSLImpl

Converts a `when` block into a when method call expression.

afterRun(DataflowProcessor, List<Object>) - Method in TaskProcessor.TaskProcessorInterceptor

afterStop(DataflowProcessor) - Method in TaskProcessor.TaskProcessorInterceptor

all(Map) - Method in ScriptBinding.ParamsMap

Renders a string containing all name-value pairs as a command line string

allScalarInputs() - Method in InputsList

allScalarValues - Field in TaskProcessor

AmazonCloudDriver - Class in nextflow.cloud.aws

Implements the cloud driver of Amazon AWS

AmazonCloudDriver(Map, AmazonEC2Client) - Constructor in AmazonCloudDriver

only for testing purpose

AmazonPriceReader - Class in nextflow.cloud.aws

Download and parse Amazon AWS cloud price CSV file

AmazonPriceReader(String) - Constructor in AmazonPriceReader

APP_BUILDNUM - Field in Const

The app build number

APP_HOME_DIR - Field in Const

The application home folder

APP_NAME - Field in Const

The application main name

APP_TIMESTAMP - Field in Const

The app build time as linux/unix timestamp

APP_TIMESTAMP_LOCAL - Field in Const

The app build time string relative to local timezone

APP_TIMESTAMP_UTC - Field in Const

The app build time string relative to UTC timezone

APP_VER - Field in Const

The application version

append0(Path, InputStream) - Method in SimpleFileCollector

Append the content of a file to the target file having key as name

append(def, def) - Method in AbstractSplitter

APPEND - Field in FileCollector

append(StringBuilder, TraceRecord) - Method in TimelineObserver

append(T) - Method in Trie

appendFormattedMessage(StringBuilder, ILoggingEvent, Throwable, Session) - Method in LoggerHelper

Find out the script line where the error has thrown

appendHelpers(StringBuilder) - Method in ContainerBuilder

appendHelpers(StringBuilder) - Method in ShifterBuilder

appendOperator(DataflowProcessor) - Method in NodeMarker

appendRunCommand(StringBuilder) - Method in ContainerBuilder

appendRunCommand(StringBuilder) - Method in ShifterBuilder

appendRunCommand(StringBuilder) - Method in UdockerBuilder

appendStream(InputStream, OutputStream) - Method in SortFileCollector

Append the content of a file to the target file having key as name

apply() - Method in AbstractSplitter

Apply the splitting operation on the given object

apply() - Method in ChoiceOp

Applies the choice operator

apply(String) - Method in CmdCloud.CreateCluster

apply(String) - Method in CmdCloud.JoinCluster

apply(String) - Method in CmdCloud.ListNodes

apply(String) - Method in CmdCloud.Shutdown

apply(String) - Method in CmdCloud.SpotPrices

apply(String) - Method in CmdCloud.SubCmd

apply(Path, Path) - Method in CmdFs.CmdCat

apply(Path, Path) - Method in CmdFs.CmdCopy

apply(Path, Path) - Method in CmdFs.CmdList

apply(Path, Path) - Method in CmdFs.CmdMove

apply(Path, Path) - Method in CmdFs.CmdRemove

apply(Path, Path) - Method in CmdFs.SubCmd

apply() - Method in CollectFileOp

apply() - Method in CollectOp

apply() - Method in CombineOp

apply() - Method in ConcatOp

apply() - Method in CrossOp

apply(Closure) - Method in DirWatcher

apply() - Method in GroupTupleOp

Main method to invoke the operator

apply() - Method in IntoOp

apply() - Method in MapOp

apply() - Method in PhaseOp

apply(Path, boolean) - Method in PublishDir

apply() - Method in RandomSampleOp

apply() - Method in SeparateOp

apply() - Method in TapOp

Apply the operator

apply(DataflowReadChannel) - Method in ToListOp

argsToOpt(Object) - Method in SplitterFactory

ArrayBag - Class in nextflow.util

A bag implementation based on an array list.

ArrayBag(Object) - Constructor in ArrayBag

ArrayTupleSerializer - Class in nextflow.util

arrive(def) - Method in Barrier

Signal the arrival of a "party"

AssetManager - Class in nextflow.scm

Handles operation on remote and local installed pipelines

AssetManager.RevisionInfo - Class in nextflow.scm

Models revision information of a project repository.

AssetManager(String, HubOptions) - Constructor in AssetManager

Create a new asset manager with the specified pipeline name

auth(URLConnection) - Method in GitlabRepositoryProvider

auth(URLConnection) - Method in RepositoryProvider

Sets the authentication credential on the connection object

autoClose - Field in AbstractSplitter

await() - Method in Session

Await the termination of all processors

await(long) - Method in TaskPollingMonitor

Await for one or more tasks to be processed

awaitCompletion() - Method in Barrier

Block until all registered parties "arrive" to the barrier condition

B

Barrier - Class in nextflow.util

An easy implementation of a barrier that wait for the "arrival" of multiple registered parties.

Barrier() - Constructor in Barrier

BaseInParam - Class in nextflow.script

Model a process generic input parameter

BaseInParam(Binding, List, short) - Constructor in BaseInParam

@param script The global script object

BaseOutParam - Class in nextflow.script

BaseOutParam(ProcessConfig) - Constructor in BaseOutParam

BaseParam - Class in nextflow.script

Base class for input/output parameters

BaseParam(Binding, List, int) - Constructor in BaseParam

BaseScript - Class in nextflow.script

Any user defined script will extends this class, it provides the base execution context

BaseScript(Binding) - Constructor in BaseScript

BASH - Field in BashWrapperBuilder

bashEnvironmentScript(Map<String, String>) - Method in TaskProcessor

Given a map holding variables key-value pairs, create a script fragment exporting the required environment variables

BashWrapperBuilder - Class in nextflow.executor

Builder to create the BASH script which is used to wrap and launch the user task

BashWrapperBuilder(TaskBean, ScriptFileCopyStrategy) - Constructor in BashWrapperBuilder

BasicMode - Enum in nextflow.script

BatchCleanup - Class in nextflow.executor

Delete cluster jobs in a batch manner

beforeRun(DataflowProcessor, List<Object>) - Method in TaskProcessor.TaskProcessorInterceptor

bind(def) - Method in BaseInParam

bind(def) - Method in EachInParam

bind(def) - Method in FileOutParam

bind(Object) - Method in SetInParam

bind(Object) - Method in SetOutParam

bind(def) - Method in ValueOutParam

binding - Field in BaseParam

binding - Field in LazyMap

The context map against which dynamic properties are resolved

bindObject - Field in BaseInParam

bindOutParam(OutParam, List) - Method in TaskProcessor

bindOutputs(TaskRun) - Method in TaskProcessor

Bind the expected output files to the corresponding output channels

BitbucketRepositoryProvider - Class in nextflow.scm

Implements a repository provider for the BitBucket service

BitbucketRepositoryProvider(String, ProviderConfig) - Constructor in BitbucketRepositoryProvider

BlankSeparatedList - Class in nextflow.util

A list of staged paths, which renders its content just separating the items by a blank space

BlankSeparatedList(Object) - Constructor in BlankSeparatedList

blocking - Field in TaskProcessor

Whenever the process execution is required to be blocking in order to handle shared object in a thread safe manner

BOOL_NO - Field in ProcessConfig

BOOL_YES - Field in ProcessConfig

broadcast(DataflowReadChannel) - Method in DataflowExtensions

buffer(DataflowReadChannel<V>, Map<String, ?>) - Method in DataflowExtensions

bufferWithSizeConstraint(DataflowReadChannel<V>, DataflowQueue, int, int, boolean) - Method in DataflowExtensions

build() - Method in BashWrapperBuilder

Build up the BASH wrapper script file which will launch the user provided script

build() - Method in CloudConfig

build() - Method in CondorExecutor.CondorWrapperBuilder

build() - Method in ConfigBuilder

@return A the application options hold in a ConfigObject instance

build() - Method in ContainerBuilder

build(StringBuilder) - Method in DockerBuilder

build() - Method in KubernetesExecutor.KubernetesWrapperBuilder

Creates the job BASH wrapper file and the Kubernetes YAML descriptor

build(StringBuilder) - Method in ShifterBuilder

build(StringBuilder) - Method in SingularityBuilder

build(StringBuilder) - Method in UdockerBuilder

buildConfig0(Map, List) - Method in ConfigBuilder

buildConfig(List<Path>) - Method in ConfigBuilder

Config file in the pipeline base dir

BytesSplitter - Class in nextflow.splitter

Splits a generic byte array in chunks having the specified length

C

cache - Field in SimpleFileCollector

CacheableCollector - Trait in nextflow.splitter

Defines a trait which can cache the produced chunks

cacheableDir(Object) - Method in Nextflow

Create a folder for the given key.

cacheableFile(Object, String) - Method in Nextflow

Create a file for the given key.

CacheBase - Trait in nextflow.cli

Common cache operations shared by CmdLog and CmdClean

CacheDB - Class in nextflow

Manages nextflow cache DB

CacheDB(UUID, String, Path) - Constructor in CacheDB

CachedTaskHandler - Class in nextflow.executor

@author Paolo Di Tommaso

CachedTaskHandler(TaskRun, TraceRecord) - Constructor in CachedTaskHandler

cacheFor(Record) - Method in CacheBase

cacheTaskAsync(TaskHandler) - Method in CacheDB

call() - Method in TaskClosure

canSubmit(TaskHandler) - Method in LocalPollingMonitor

Determines if a task can be submitted for execution checking if the resources required (cpus and memory) match the amount of avail resource

canSubmit(TaskHandler) - Method in TaskPollingMonitor

Defines the strategy determining if a task can be submitted for execution.

capture(Closure) - Method in CaptureProperties

CaptureProperties - Class in nextflow.extension

Hack to capture the names of referenced variables into a closure

CascadingConfig - Class in nextflow.config

Configuration object which fallback to a parent CascadingConfig object when an attribute value is missing.

CascadingConfig(Map<K, V>, CascadingConfig<K, V>) - Constructor in CascadingConfig

chain(DataflowReadChannel<?>, Map<String, Object>, Closure<V>) - Method in DataflowExtensions

Chain operator, this is a synonym of DataflowReadChannel.chainWith

chainImpl(DataflowReadChannel<?>, DataflowReadChannel<V>, Map, Closure<V>) - Method in DataflowHelper

Channel - Class in nextflow

Channel factory object

channel() - Method in AbstractSplitter

@return Split the target object and return a channel emitting the produced chunks

channel(Collection) - Method in DataflowExtensions

Creates a channel emitting the entries in the collection to which is applied

channel(Object) - Method in Nextflow

Create a DataflowQueue populating with a single value

channel() - Method in SplitterStrategy

CharSequenceCollector - Class in nextflow.splitter

A collector strategy that creates a string chunks

charset - Field in AbstractTextSplitter

checkActiveStatus(def, def) - Method in AbstractGridExecutor

Verify that a job in a 'active' state i.e.

checkAllTasks() - Method in TaskPollingMonitor

Check and update the status of queued tasks

checkCached() - Method in CacheableCollector

checkCachedOrLaunchTask(TaskRun, HashCode, boolean) - Method in TaskProcessor

Try to check if exists a previously executed process result in the a cached folder.

checkCachedOutput(TaskRun, Path, HashCode) - Method in TaskProcessor

Check whenever the outputs for the specified task already exist

checkErrorStrategy(TaskRun, ProcessException, int, int) - Method in TaskProcessor

checkExistsById(UUID) - Method in HistoryFile

checkExistsByName(String) - Method in HistoryFile

checkField(K) - Method in CascadingConfig

checkForHelp() - Method in Launcher

checkIfCompleted() - Method in CachedTaskHandler

checkIfCompleted() - Method in GridTaskHandler

checkIfCompleted() - Method in LocalTaskHandler

Check if the submitted job has terminated its execution

checkIfCompleted() - Method in NativeTaskHandler

checkIfCompleted() - Method in NopeTaskHandler

checkIfCompleted() - Method in TaskHandler

Model the start transition from #STARTED to TERMINATED

checkIfRunning() - Method in CachedTaskHandler

checkIfRunning() - Method in GridTaskHandler

checkIfRunning() - Method in LocalTaskHandler

Check if the submitted job has started

checkIfRunning() - Method in NativeTaskHandler

checkIfRunning() - Method in NopeTaskHandler

checkIfRunning() - Method in TaskHandler

Model the start transition from #SUBMITTED to STARTED

checkout(String) - Method in AssetManager

Checkout a specific revision

checkoutRemoteBranch(String) - Method in AssetManager

checkResponse(HttpURLConnection) - Method in RepositoryProvider

Check for response error status.

checkStoredOutput(TaskRun) - Method in TaskProcessor

Check if exists a *storeDir* for the specified task.

checkTaskStatus(TaskHandler) - Method in TaskPollingMonitor

Check the status of the given task

checkValidProfile(Collection<String>) - Method in ConfigBuilder

checkValidRemoteRepo() - Method in AssetManager

checkWhenGuard(TaskRun) - Method in TaskProcessor

choice(DataflowReadChannel, List<DataflowWriteChannel<T>>, Closure<Integer>) - Method in DataflowExtensions

ChoiceOp - Class in nextflow.extension

Implements the logic for DataflowExtensions.choice operator(s)

ChoiceOp(DataflowReadChannel, List<DataflowWriteChannel>, Closure<Integer>) - Constructor in ChoiceOp

Creates the choice operator

CirrusExecutor - Class in nextflow.executor

Executor for ClusterK Cirrus scheduler

CirrusFileCopyStrategy - Class in nextflow.executor

Defines the script operation to handle file when running in the Cirrus cluster

CirrusFileCopyStrategy(TaskBean) - Constructor in CirrusFileCopyStrategy

CirrusTaskHandler - Class in nextflow.executor

cleanUp() - Method in Session

cleanup() - Method in TaskPollingMonitor

Kill all pending jobs when current execution session is aborted

CliOptions - Class in nextflow.cli

Main application command line options

clone(File, String) - Method in AssetManager

Clone a pipeline from a remote pipeline repository to the specified folder

clone() - Method in TaskBean

clone() - Method in TaskClosure

clone() - Method in TaskConfig

clone() - Method in TaskContext

clone() - Method in TaskRun

close() - Method in AssetManager

Close the underlying Git repository

close() - Method in CacheDB

Close the underlying database and index file

close(DataflowReadChannel) - Method in DataflowExtensions

Close a dataflow queue channel binding a Channel.STOP item

close() - Method in FileCollector

Close the collector deleting temporary files

close() - Method in LevelDbSort

Shutdown the DB and remove temporary files

close() - Method in RemoteSession

Close the session i.e. delete all temporary directories

close() - Method in SequentialFileStore

close() - Method in SortFileCollector

Close sorting structures instance and cleanup temporary files

close() - Method in TextFileCollector

closure - Field in AbstractSplitter

CloudConfig - Class in nextflow.cloud

Holds the cloud configuration settings provided in the `nextflow.config` file in the `cloud` scope

CloudConfig.Autoscale - Class in nextflow.cloud

Model the configuration of the cloud auto-scaling feature

CloudConfig.Autoscale(Map, LaunchConfig) - Constructor in CloudConfig.Autoscale

CloudConfig.EnvConfig - Class in nextflow.cloud

Fetch the cloud config setting in the system environment adding to each attribute the `NXF_CLOUD_` prefix

CloudConfig.EnvConfig(Map) - Constructor in CloudConfig.EnvConfig

CloudConfig.Nextflow - Class in nextflow.cloud

Wrap the nextflow configuration settings in the cloud scope e.g.

CloudConfig.Nextflow(Map) - Constructor in CloudConfig.Nextflow

CloudConfig(Map, CascadingConfig<String, Object>) - Constructor in CloudConfig

CloudConst - Class in nextflow.cloud

Constants for the cloud module

CloudDriver - Trait in nextflow.cloud

Defines the cloud driver interface methods

CloudDriverFactory - Class in nextflow.cloud

Factory class to get and instance of a concrete CloudDriver object

CloudInstance - Class in nextflow.cloud.types

Model a cloud instance

CloudInstanceStatus - Enum in nextflow.cloud.types

Model a cloud instance status

CloudInstanceType - Class in nextflow.cloud.types

Models a cloud instance type

CloudSpotPrice - Class in nextflow.cloud.types

Models an instance spot price record

CloudSpotTerminationException - Class in nextflow.cloud

Exception thrown when a spot instance is retired by the provider

CloudSpotTerminationException(String) - Constructor in CloudSpotTerminationException

ClusterConfig - Class in nextflow.util

Helper class retrieve cluster configuration properties

ClusterConfig(Map, String, Map) - Constructor in ClusterConfig

CMD_CONDOR - Field in CondorExecutor

CMD_ENV - Field in TaskRun

CMD_ERRFILE - Field in TaskRun

CMD_EXIT - Field in TaskRun

CMD_INFILE - Field in TaskRun

CMD_K8S - Field in KubernetesExecutor

CMD_LOG - Field in TaskRun

CMD_OUTFILE - Field in TaskRun

CMD_RUN - Field in TaskRun

CMD_SCRIPT - Field in TaskRun

CMD_START - Field in TaskRun

CMD_STUB - Field in TaskRun

CMD_TRACE - Field in TaskRun

CmdBase - Class in nextflow.cli

Implement command shared methods

CmdClean - Class in nextflow.cli

Implements cache clean up command

CmdClone - Class in nextflow.cli

CLI sub-command clone

CmdCloud - Class in nextflow.cli

Implements the `cloud` command

CmdCloud.CreateCluster - Class in nextflow.cli

Implements the cloud `launch-cluster` sub-command

CmdCloud.JoinCluster - Class in nextflow.cli

Implements the cloud `launch-nodes` sub-command

CmdCloud.ListNodes - Class in nextflow.cli

Implements the cloud `list-node` sub-command

CmdCloud.Shutdown - Class in nextflow.cli

Implements the cloud `shutdown` sub-command

CmdCloud.SpotPrices - Class in nextflow.cli

Implements the cloud `spot-prices` sub-command

CmdCloud.SubCmd - Interface in nextflow.cli

CmdCloud() - Constructor in CmdCloud

CmdConfig - Class in nextflow.cli

Prints the pipeline configuration

CmdDrop - Class in nextflow.cli

CLI sub-command DROP

CmdFs - Class in nextflow.cli

Implements `fs` command

CmdFs.CmdCat - Class in nextflow.cli

CmdFs.CmdCopy - Class in nextflow.cli

CmdFs.CmdList - Class in nextflow.cli

CmdFs.CmdMove - Class in nextflow.cli

CmdFs.CmdRemove - Class in nextflow.cli

CmdFs.SubCmd - Trait in nextflow.cli

CmdHelp - Class in nextflow.cli

CLI sub-command HELP

CmdHelper - Class in nextflow.cli

Cmd CLI helper methods

CmdHistory - Class in nextflow.cli

CLI sub-command HISTORY

CmdInfo - Class in nextflow.cli

CLI sub-command INFO

CmdList - Class in nextflow.cli

CLI sub-command LIST.

CmdLog - Class in nextflow.cli

Implements the `log` command to print tasks runtime information of an execute pipeline

CmdLs - Class in nextflow.cli

@author Paolo Di Tommaso

CmdNode - Class in nextflow.cli

CLI-command NODE

CmdPull - Class in nextflow.cli

CLI sub-command PULL

CmdRun - Class in nextflow.cli

CLI sub-command RUN

CmdRun.DurationConverter - Class in nextflow.cli

CmdSelfUpdate - Class in nextflow.cli

Self-update command

CmdView - Class in nextflow.cli

CLI sub-command VIEW -- Print a pipeline script to console

collate(DataflowReadChannel<V>, int, int, boolean) - Method in DataflowExtensions

collect(DataflowReadChannel<V>, Map, Closure) - Method in DataflowExtensions

collectFile(DataflowReadChannel, Map, Closure) - Method in DataflowExtensions

CollectFileOp - Class in nextflow.extension

Implements the body of DataflowExtensions.collectFile operator

CollectFileOp(DataflowReadChannel, Map, Closure) - Constructor in CollectFileOp

collectName - Field in AbstractTextSplitter

CollectOp - Class in nextflow.extension

Implements DataflowExtensions.collect operator

CollectOp(DataflowReadChannel, Closure, Map) - Constructor in CollectOp

CollectorStrategy - Interface in nextflow.splitter

Defines an abstract contract to collect items produced by splitters into chunks

collectOutFiles(TaskRun, FileOutParam, Path, Map) - Method in TaskProcessor

collectOutputs(TaskRun, Path, def, Map) - Method in TaskProcessor

Once the task has completed this method is invoked to collected all the task results

collectOutValues(TaskRun, ValueOutParam, Map) - Method in TaskProcessor

collectPath - Field in AbstractTextSplitter

collectStdOut(TaskRun, StdOutParam, def) - Method in TaskProcessor

Collects the process 'std output'

columnsHeader - Field in CsvSplitter

Defines the columns names of the resulting records

combine(DataflowReadChannel, Map, Object) - Method in DataflowExtensions

CombineOp - Class in nextflow.extension

Implements the DataflowExtensions.spread operator

CombineOp.KeyPair - Class in nextflow.extension

CombineOp(DataflowReadChannel, Object) - Constructor in CombineOp

command(String) - Method in Launcher

compare(IndexEntry, IndexEntry) - Method in SortFileCollector.IndexSort

compareTo(Object) - Method in TaskId

completed - Field in TaskProcessor

Flag set true when the processor termination has been invoked

ComposedConfigScript - Class in nextflow.config

Extends a groovy.lang.Script class adding a method that allows a configuration file to include other configuration files.

ComposedConfigSlurper - Class in nextflow.config

A ConfigSlurper that allows to include a config file into another.

ComposedConfigSlurper(String) - Constructor in ComposedConfigSlurper

Constructs a new IncludeConfigSlurper instance using the given environment

composeVolumePath(String) - Method in ContainerBuilder

composeVolumePath(String) - Method in DockerBuilder

concat(DataflowReadChannel, DataflowReadChannel) - Method in DataflowExtensions

Creates a channel that emits the items in same order as they are emitted by two or more channel

ConcatOp - Class in nextflow.extension

Implements the DataflowExtensions.concat operator

ConcatOp(DataflowReadChannel, DataflowReadChannel) - Constructor in ConcatOp

CondorExecutor - Class in nextflow.executor

HTCondor executor

CondorExecutor.CondorWrapperBuilder - Class in nextflow.executor

config - Field in CascadingConfig

config - Field in RepositoryProvider

Holds the provider configuration

config - Field in TaskProcessor

The corresponding task configuration properties, it holds the inputs/outputs definition as well as other execution meta-declaration

ConfigBuilder - Class in nextflow.config

Builds up the Nextflow configuration object

ConfigField - Annotation Type in nextflow.config

Annotation used to marked fields of CascadingConfig subclasses

ConfigHelper - Class in nextflow.util

Helper method to handle configuration object

ConfigParseException - Class in nextflow.exception

Exception thrown when it failed to parse the configuration file

configProperties - Field in ProcessConfig

configureLogger(CliOptions, boolean) - Method in LoggerHelper

Const - Class in nextflow

Application main constants

ContainerBuilder - Class in nextflow.container

Base class for container wrapper builders

ContainerConfig - Class in nextflow.container

Models container engine configuration

ContainerConfig(Map) - Constructor in ContainerConfig

containerInit() - Method in BashWrapperBuilder

Setup container related variables

containerInit() - Method in KubernetesExecutor.KubernetesWrapperBuilder

Container execution is managed by Kubernetes thus disable the execution through the job wrapper script

ContainerScriptTokens - Class in nextflow.container

Hold container definition parsed in a shell script

containsAttribute(K) - Method in CascadingConfig

containsKey(String) - Method in SimpleFileCollector

containsKey(String) - Method in TraceRecord

controlMessageArrived(DataflowProcessor, DataflowReadChannel<Object>, int, Object) - Method in TaskProcessor.TaskProcessorInterceptor

convert(String) - Method in CmdRun.DurationConverter

convertInputMethod(Expression) - Method in NextflowDSLImpl

convertOutputMethod(Expression) - Method in NextflowDSLImpl

convertProcessBlock(MethodCallExpression, SourceUnit) - Method in NextflowDSLImpl

This transformation applies to tasks code block and translate the script string to be executed wrapping it by a closure

convertProcessDef(MethodCallExpression, SourceUnit) - Method in NextflowDSLImpl

This method handle the process definition, so that it transform the user entered syntax process myName ( named: args, .. ) { code .. }

copyFile(String, Path) - Method in CirrusFileCopyStrategy

{@inheritDoc}

copyFile(String, Path) - Method in S3FileCopyStrategy

{@inheritDoc}

copyFile(String, Path) - Method in ScriptFileCopyStrategy

The command to copy a path to the specified target folder

copyFile(String, Path) - Method in SimpleFileCopyStrategy

{@inheritDoc}

copyPublicAttributes() - Method in CascadingConfig

count - Field in AbstractSplitter

count(DataflowReadChannel<?>, Object) - Method in DataflowExtensions

Counts the number of occurrences which satisfy the given closure from inside this collection

count() - Method in SplitterStrategy

countBy(DataflowReadChannel<?>, Closure) - Method in DataflowExtensions

Sorts all collection members into groups determined by the supplied mapping closure and counts the group size

countOverChannel(DataflowReadChannel, SplitterStrategy, Map) - Method in SplitterFactory

Implements dynamic method extension for counter operators

cpus - Field in ContainerBuilder

create() - Method in Channel

Create an new channel

create(Map) - Method in CloudConfig

create(def, LaunchConfig) - Method in CloudConfig.Autoscale

Class factory method.

create() - Method in KubernetesExecutor.YamlBuilder

create() - Method in LevelDbSort

Creates a DB instance

create(Session, String) - Method in LocalPollingMonitor

Creates an instance of LocalPollingMonitor

create(def) - Method in PublishDir

Object factory method

create(ProviderConfig, String) - Method in RepositoryProvider

Factory method

create(Class<T>) - Method in SetOutParam

create(Class<? extends SplitterStrategy>, String) - Method in SplitterFactory

Creates a splitter object by specifying the splitter class

create(Session, String, Duration) - Method in TaskPollingMonitor

createBashTaskHandler(TaskRun) - Method in LocalExecutor

createBashWrapperBuilder(TaskRun) - Method in AbstractGridExecutor

createBashWrapperBuilder(TaskRun) - Method in CirrusExecutor

createBashWrapperBuilder(TaskRun) - Method in CondorExecutor

createBashWrapperBuilder(TaskRun) - Method in CrgExecutor

createBashWrapperBuilder(TaskRun) - Method in KubernetesExecutor

createCallbackWrapper(int, Closure) - Method in TaskProcessor

Wraps the target method by a closure declaring as many arguments as many are the user declared inputs object.

createCollector() - Method in AbstractSplitter

Returns:

create a new CollectorStrategy object.

createCollector() - Method in AbstractTextSplitter

@return A CollectorStrategy object implementing a concrete strategy according the user provided options

createCollector() - Method in BytesSplitter

createCollector() - Method in CsvSplitter

createConsoleAppender() - Method in LoggerHelper

createDagObserver(Collection<TraceObserver>) - Method in Session

createDefault() - Method in ProviderConfig

createEncoder() - Method in LoggerHelper

createExtraeObserver(Collection<TraceObserver>) - Method in Session

create the Extrae trace observer

createFileAppender() - Method in LoggerHelper

createFileCollector() - Method in CollectFileOp

createForwardWrapper(int, List) - Method in TaskProcessor

Implements the closure which *combines* all the iteration

createLogger(String, Level) - Method in LoggerHelper

createNativeTaskHandler(TaskRun) - Method in LocalExecutor

createOperator() - Method in TaskProcessor

Verify if this process run only one time

createPool(boolean, int) - Method in CustomPoolFactory

createProcessBuilder() - Method in CirrusTaskHandler

createProcessBuilder() - Method in GridTaskHandler

createProcessor(String, Closure, Map) - Method in ProcessFactory

Create a task processor

createRollingAppender() - Method in LoggerHelper

createTaskHandler(TaskRun) - Method in AbstractGridExecutor

createTaskHandler(TaskRun) - Method in CirrusExecutor

createTaskHandler(TaskRun) - Method in Executor

@return Create a new TaskHandler to manage the scheduling actions for this task

createTaskHandler(TaskRun) - Method in LocalExecutor

createTaskHandler(TaskRun) - Method in NopeExecutor

createTaskHashKey(TaskRun) - Method in TaskProcessor

createTaskMonitor() - Method in AbstractGridExecutor

Create a a queue holder for this executor @return

createTaskMonitor() - Method in CirrusExecutor

Create a a queue holder for this executor @return

createTaskMonitor() - Method in Executor

@return Create a new instance of the TaskQueueHolder component

createTaskMonitor() - Method in LocalExecutor

createTaskMonitor() - Method in NopeExecutor

createTaskRun() - Method in TaskProcessor

Create a new TaskRun instance, initializing the following properties :

TaskRun#id

TaskRun#status

TaskRun#index

TaskRun#name

TaskRun#process

createTempDir() - Method in FileCollector

Create the temporary directory

createTemplate(Reader) - Method in TaskTemplateEngine

createTimelineObserver(Collection<TraceObserver>) - Method in Session

Create timeline report file observer

createTraceFileObserver(Collection<TraceObserver>) - Method in Session

createVisitor(SourceUnit) - Method in NextflowDSLImpl

CrgExecutor - Class in nextflow.executor

An executor specialised for CRG cluster

cross(DataflowReadChannel, DataflowReadChannel, Closure) - Method in DataflowExtensions

CrossOp - Class in nextflow.extension

Implements the DataflowExtensions.cross operator logic

CrossOp(DataflowReadChannel, DataflowReadChannel) - Constructor in CrossOp

CsvSplitter - Class in nextflow.splitter

Split a CSV file in records

currentLabel - Field in NextflowDSLImpl

currentTask - Field in TaskProcessor

Keeps track of the task instance executed by the current thread

currentTaskName - Field in NextflowDSLImpl

CustomPoolFactory - Class in nextflow.util

A configurable thread pool factory

CustomThreadPool - Class in nextflow.util

Implements a resizeable unbounded Thread pool executor

CytoscapeHtmlRenderer - Class in nextflow.dag

Render the DAG in HTML using Cytoscape.js to the specified file.

CytoscapeJsRenderer - Class in nextflow.dag

Render the DAG in Cytoscape.js compatible JSON to the specified file.

D

DaemonLauncher - Interface in nextflow.daemon

Generic interface to launch the cluster daemon

DAG - Class in nextflow.dag

Model a direct acyclic graph of the pipeline execution.

DAG.ChannelHandler - Class in nextflow.dag

A simple wrapper object to handle a channel and the associated label

DagRenderer - Interface in nextflow.dag

Base interface to render a graph document

DataflowExtensions - Class in nextflow.extension

A set of operators inspired to RxJava extending the methods available on DataflowChannel data structure

DataflowHelper - Class in nextflow.extension

This class provides helper methods to implement nextflow operators

DATETIME_FORMAT - Field in Const

The date time formatter string

decide(ILoggingEvent) - Method in LoggerHelper.ConsoleLoggerFilter

DECODE_STATUS - Field in CondorExecutor

DECODE_STATUS - Field in NqsiiExecutor

DECODE_STATUS - Field in SgeExecutor

decodeInputs(List) - Method in BaseInParam

decodeInputs(List) - Method in InParam

decompress - Field in AbstractSplitter

DEF_FILE_NAME - Field in GraphObserver

DEFAULT_BRANCH - Field in AssetManager

DEFAULT_EXECUTOR - Field in ProcessFactory

DEFAULT - Field in HistoryFile

DEFAULT_HUB - Field in AssetManager

DEFAULT_MAIN_FILE_NAME - Field in AssetManager

DEFAULT_ORGANIZATION - Field in AssetManager

DEFAULT_PROFILE - Field in ConfigBuilder

DEFAULT_ROOT - Field in AssetManager

DefaultInParam - Class in nextflow.script

DefaultInParam(ProcessConfig) - Constructor in DefaultInParam

DefaultOutParam - Class in nextflow.script

DefaultOutParam(ProcessConfig) - Constructor in DefaultOutParam

defineHashingParams() - Method in CollectFileOp

defineStoreDirAndFileName() - Method in CollectFileOp

dehydrate() - Method in TaskContext

Serialize the DelegateMap instance to a byte array

deleteEntry0(HistoryFile.Record) - Method in HistoryFile

deleteEntry(HistoryFile.Record) - Method in HistoryFile

deleteIndex() - Method in CacheDB

deltaLocal() - Method in Const

describeInstanceType(String) - Method in AmazonCloudDriver

Describe an instance type by the given type

describeInstanceType(String) - Method in CloudDriver

Retrieve a CloudInstanceType object for the given instance type

deserialize(byte[], ClassLoader) - Method in KryoHelper

deserialize(TaskProcessor, byte[]) - Method in TaskContext

deserialize(byte[]) - Method in TraceRecord

destroy() - Method in LocalTaskHandler

Destroy the process handler, closing all associated streams

destroy() - Method in Session

detectQualityString(String) - Method in FastqSplitter

DIRECTIVES - Field in ProcessConfig

DirWatcher - Class in nextflow.file

Watch the content of a directory for file system events

DirWatcher(String, String, String, boolean, String, FileSystem) - Constructor in DirWatcher

distinct(DataflowReadChannel<V>, Closure<?>) - Method in DataflowExtensions

suppress duplicate consecutive items emitted by the source Observable

DockerBuilder - Class in nextflow.container

Helper methods to handle Docker containers

DockerBuilder(String) - Constructor in DockerBuilder

doLayout(ILoggingEvent) - Method in LoggerHelper.PrettyConsoleLayout

DotRenderer - Class in nextflow.dag

Render the DAG using the Graphviz DOT format to the specified file.

DotRenderer(String) - Constructor in DotRenderer

Create a render instance

doubleValue() - Method in TaskId

download(String) - Method in AssetManager

Download a pipeline from a remote Github repository

DripMain - Class in nextflow.cli

Drip bootstrap entry point

drop() - Method in CacheDB

dumpActiveNodes() - Method in DAG

@return A string listing the current active processes/operators in the dataflow network represented by this DAG

dumpLogFile(int) - Method in TaskRun

dumpNetworkStatus() - Method in Session

Dump the current dataflow network listing the status of active processes and operators for debugging purpose

dumpObject(def, int) - Method in TaskRun

dumpStderr(int) - Method in TaskRun

dumpStdout(int) - Method in TaskRun

Dump the first max line of the task #stdout

dumpTerminationStatus() - Method in TaskProcessor

Dump the current process status listing all input *port* statuses for debugging purpose

E

each(Closure) - Method in AbstractSplitter

Apply the specified closure to each chunk in the target object

each(Closure) - Method in SplitterStrategy

EachInParam - Class in nextflow.script

Represents a process input *iterator* parameter

eachInstance(Closure) - Method in AmazonCloudDriver

eachInstance(Closure) - Method in CloudDriver

Iterate over the list of available instances

eachInstanceWithIds(List<String>, Closure) - Method in AmazonCloudDriver

eachInstanceWithIds(List<String>, Closure) - Method in CloudDriver

Iterate over the list of instances for the instance IDs

eachInstanceWithTags(Map, Closure) - Method in AmazonCloudDriver

eachInstanceWithTags(Map, Closure) - Method in CloudDriver

Iterate over the list of instances for the given tags

eachRecord(Closure) - Method in CacheDB

Iterate the tasks cache using the index file

eachRow(Closure) - Method in HistoryFile

eachSpotPrice(List<String>, Closure) - Method in AmazonCloudDriver

eachSpotPrice(Closure) - Method in CloudDriver

Iterate over list of spot prices for the given instance types

echo(boolean) - Method in BaseScript

Enable disable task 'echo' configuration property

echo(def) - Method in ProcessConfig

echoStdout() - Method in TaskRun

Print to the current system console the task produced stdout

elapsedTimeMillis() - Method in LocalTaskHandler

elem - Field in AbstractSplitter

emitItems(def) - Method in CollectFileOp

empty() - Method in Channel

Create a empty channel i.e. only emits a STOP signal

ENDPOINT - Field in AmazonPriceReader

engineOptions - Field in ContainerBuilder

env - Field in ContainerBuilder

EnvInParam - Class in nextflow.script

Represents a process *environment* input parameter

equals(Object) - Method in TaskId

equals(Object) - Method in TraceRecord

error(String) - Method in Nextflow

Throws a script runtime error

ErrorStrategy - Enum in nextflow.processor

Strategies to handle a process execution fault

ErrorStrategy(boolean) - Constructor in ErrorStrategy

errorStrategy(def) - Method in ProcessConfig

evict(TaskHandler) - Method in TaskMonitor

Remove the TaskHandler instance from the queue of tasks to be processed

evict(TaskHandler) - Method in TaskPollingMonitor

Evicts a task from the processing tasks queue

execute(List<String>) - Method in ScriptRunner

Execute a Nextflow script, it does the following:

parse the script

launch script execution

await for all tasks completion

Executor - Class in nextflow.executor

Declares methods have to be implemented by a generic execution strategy

executor - Field in TaskProcessor

The underlying executor which will run the task

executorsMap - Field in ProcessFactory

exit(String) - Method in Nextflow

Stop the current execution returning a 0 error code and the specified message

exitFile(Path) - Method in CirrusFileCopyStrategy

{@inheritDoc}

exitFile(Path) - Method in S3FileCopyStrategy

{@inheritDoc}

exitFile(Path) - Method in ScriptFileCopyStrategy

@param file The java.nio.file.Path to the exit file

exitFile(Path) - Method in SimpleFileCopyStrategy

{@inheritDoc}

expandWildcards(String, List<FileHolder>) - Method in TaskProcessor

An input file name may contain wildcards characters which have to be handled coherently given the number of files specified.

ExtraeTraceObserver - Class in nextflow.trace

Profile observer producing an Extra tracing file

F

FailedGuardException - Class in nextflow.exception

Exception thrown when a task guard condition e.g.

FailedGuardException(String, String, Throwable) - Constructor in FailedGuardException

fakeInput() - Method in ProcessConfig

Defines a special *dummy* input parameter, when no inputs are provided by the user for the current task

fakeOutput() - Method in ProcessConfig

fasta(def) - Method in Nextflow

Creates a FASTA splitter handler for the given object

FastaSplitter - Class in nextflow.splitter

Split FASTA formatted text content or files

fastq(def) - Method in Nextflow

Creates a FASTQ splitter handler for the given object

FastqSplitter - Class in nextflow.splitter

Split FASTQ formatted text content or files

fault(TaskFault, TaskHandler) - Method in Session

Halt the pipeline execution choosing exiting immediately or completing current pending task depending the chosen ErrorStrategy

fetchContainers() - Method in ScriptRunner

fetchInterpreter(String) - Method in TaskProcessor

Given the task script extract the top *she-bang* interpreter declaration removing the #!

fetchRecord(BufferedReader) - Method in AbstractTextSplitter

Read and parse a new record from the reader object

fetchRecord(BufferedReader) - Method in CsvSplitter

Process a CSV row at time

fetchRecord(BufferedReader) - Method in FastaSplitter

fetchRecord(BufferedReader) - Method in FastqSplitter

fetchRecord(BufferedReader) - Method in StringSplitter

fetchRecord(BufferedReader) - Method in TextSplitter

A record is a text line

fetchValue(String, String) - Method in PbsExecutor

fetchVariables(ClosureExpression, SourceUnit) - Method in NextflowDSLImpl

Fetch all the variable references in a closure expression.

FIELDS - Field in TraceRecord

FILE_NAME - Field in HistoryFile

file(Map, def) - Method in Nextflow

Get one or more file object given the specified path or glob pattern.

FileCollector - Class in nextflow.file

File collector base class

FileCollector() - Constructor in FileCollector

FileInParam - Class in nextflow.script

Represents a process *file* input parameter

fileMode - Field in AbstractTextSplitter

FileOutParam - Class in nextflow.script

Model a process *file* output parameter

FileOutParam(Map) - Constructor in FileOutParam

ONLY FOR TESTING DO NOT USE

filePattern - Field in FileInParam

files(Map, def) - Method in Nextflow

FileSerializer - Class in nextflow.util

fileStr(Path) - Method in CirrusFileCopyStrategy

{@inheritDoc}

fileStr(Path) - Method in S3FileCopyStrategy

{@inheritDoc}

fileStr(Path) - Method in ScriptFileCopyStrategy

@param file A file java.nio.file.Path

fileStr(Path) - Method in SimpleFileCopyStrategy

{@inheritDoc}

filter(DataflowReadChannel<T>, Closure<Boolean>) - Method in DataflowExtensions

find(String) - Method in AssetManager

findAfter(String) - Method in HistoryFile

findAll() - Method in HistoryFile

findAllRunNames() - Method in HistoryFile

findBefore(String) - Method in HistoryFile

findBut(String) - Method in HistoryFile

findById(String) - Method in HistoryFile

findByIdOrName(String) - Method in HistoryFile

findCommand(String) - Method in Launcher

findInterfaceAddressesByName(String) - Method in ClusterConfig

findNameByClass(Class<Executor>) - Method in ProcessFactory

Extract the executor name by using the annotation ServiceName or fallback to simple classname if the annotation is not provided

first(DataflowReadChannel<V>, Object) - Method in DataflowExtensions

Emit only the first item emitted by a channel, or the first item that meets some condition

firstLineAsHeader - Field in CsvSplitter

When true parse the first line as the columns names

fixDirectiveWithNegativeValue(Statement) - Method in NextflowDSLImpl

fixEqualsOp(String) - Method in CmdHelper

Expand single `=` to `==` in filter string

fixGuards(Statement, SourceUnit) - Method in NextflowDSLImpl

fixLazyGString(Statement) - Method in NextflowDSLImpl

fixMethodCall(MethodCallExpression) - Method in NextflowDSLImpl

This method converts the a method call argument from a Variable to a Constant value so that it is possible to reference variable that not yet exist

fixOwnership() - Method in BashWrapperBuilder

fixOwnership() - Method in KubernetesExecutor.KubernetesWrapperBuilder

fixStdinStdout(ExpressionStatement) - Method in NextflowDSLImpl

flatMap(DataflowReadChannel<?>, Closure<V>) - Method in DataflowExtensions

Transform the items emitted by a channel by applying a function to each of them and then flattens the results of that function.

flatten(DataflowReadChannel) - Method in DataflowExtensions

flip() - Method in SequentialFileStore

Turn the buffer in read mode

floatValue() - Method in TaskId

followLinks - Field in FileOutParam

When true it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: true)

fOptionsMap - Field in AbstractSplitter

force(Object, Object) - Method in ReadOnlyMap

Overrides a map value even if it's declared as read-only

forceTermination() - Method in Barrier

Force the barrier termination

formatGuardError(List, FailedGuardException, TaskRun) - Method in TaskProcessor

formatRef(Ref, String, String, boolean, int) - Method in AssetManager

formatTaskError(List, Throwable, TaskRun) - Method in TaskProcessor

FORMATTER - Field in TraceRecord

fQueueStatus - Field in AbstractGridExecutor

Store jobs status

from(Object) - Method in BaseInParam

from(Object) - Method in Channel

Creates a channel sending the items in the collection over it

from(Object) - Method in InParam

fromFilePairs(Map, def, Closure) - Method in Channel

fromObject - Field in BaseInParam

fromPath(Map, def) - Method in Channel

G

generateNextName() - Method in HistoryFile

get(def) - Method in LazyMap

Override the get method in such a way that groovy.lang.Closure values are resolved against the binding map

get(long) - Method in LevelDbSort

Retrieve an object from the DB

get(Object) - Method in ScriptBinding.ParamsMap

get(int) - Method in ScriptRunner.ArgsList

get(String) - Method in SimpleFileCollector

get(String) - Method in TaskConfig

get(Object) - Method in TaskContext

get(String) - Method in TraceRecord

getAddress() - Method in CloudInstance

@return The instance public address, falling back on the private when the public is not available

getAfter() - Method in CacheBase

getAllChunks() - Method in CacheableCollector

getAllVariables() - Method in NextflowDSLImpl.VariableVisitor

Returns:

The set of all variables referenced in the script.

getArgs() - Method in CacheBase

getArity() - Method in CmdFs.CmdCat

getArity() - Method in CmdFs.CmdCopy

getArity() - Method in CmdFs.CmdList

getArity() - Method in CmdFs.CmdMove

getArity() - Method in CmdFs.CmdRemove

getArity() - Method in CmdFs.SubCmd

getAt(int) - Method in BlankSeparatedList

getAt(int) - Method in ScriptRunner.ArgsList

getAttempt() - Method in TaskConfig

getAttribute(K, V) - Method in CascadingConfig

getAttribute(String) - Method in CloudConfig.EnvConfig

getAttribute(String, def) - Method in ClusterConfig

getAttributeNames() - Method in CascadingConfig

getAttributeNames(String) - Method in ClusterConfig

getAutoscale() - Method in CloudConfig

getAwsCredentials() - Method in CirrusExecutor

getBarrier() - Method in Session

getBaseDir(String) - Method in CmdConfig

getBaseName() - Method in AssetManager

getBefore() - Method in CacheBase

getBeforeStartScript() - Method in CirrusFileCopyStrategy

@return A script snipped that download from S3 the task scripts: .command.env, .command.sh, .command.in, etc.

getBeforeStartScript() - Method in S3FileCopyStrategy

@return A script snipped that download from S3 the task scripts: .command.env, .command.sh, .command.in, etc.

getBeforeStartScript() - Method in ScriptFileCopyStrategy

@return A BASH snippet included in the wrapper script to be executed *before* the task execution itself

getBeforeStartScript() - Method in SimpleFileCopyStrategy

getBinding() - Method in Session

getBinDir() - Method in Session

The folder where script binaries file are located, by default the folder 'bin' in the script base directory

getBootStorageSize() - Method in LaunchConfig

getBut() - Method in CacheBase

getByName(String) - Method in HistoryFile

Lookup a session ID given a `run` name string

getCache() - Method in Session

getCacheableOptions() - Method in AbstractTextSplitter

@return A map of the options that contribute to create unique key

getCapacity() - Method in TaskPollingMonitor

@return the current capacity value by the number of slots specified

getChannels() - Method in InputsList

getChannels() - Method in OutputsList

getCharset() - Method in AbstractTextSplitter

getChild(T) - Method in Trie

getChildren() - Method in Trie

getChunk() - Method in CharSequenceCollector

getChunk() - Method in CollectorStrategy

@return The chunk made up of the added items

getChunk() - Method in ObjectListCollector

getChunk() - Method in TextFileCollector

getClassLoader() - Method in Session

getCliString() - Method in Launcher

getCloneUrl() - Method in BitbucketRepositoryProvider

getCloneUrl() - Method in GithubRepositoryProvider

{@inheritDoc}

getCloneUrl() - Method in GitlabRepositoryProvider

{@inheritDoc}

getCloneUrl() - Method in LocalRepositoryProvider

getCloneUrl() - Method in RepositoryProvider

@return The repository URL used by Git to clone the remote repository e.g. https://github.com/nextflow-io/hello.git

getCloudDriverName() - Method in ClusterConfig

getClusterJoin() - Method in ClusterConfig

getClusterName() - Method in LaunchConfig

getClusterOptionsAsList() - Method in TaskConfig

@return Parse the clusterOptions configuration option and return the entries as a list of values

getCollector() - Method in AbstractSplitter

@return The current CollectorStrategy object

getCommitId() - Method in ScriptFile

@return The repository commitId

getConditionalBlockNames() - Method in ComposedConfigSlurper

@return When a conditional block is registered this method returns the collection of block names visited during the parsing

getConditionalBlockValues() - Method in ComposedConfigSlurper

getConfig() - Method in BaseScript

Holds the configuration object which will used to execution the user tasks

getConfig() - Method in ClusterConfig

getConfig() - Method in ScriptBinding

getConfig() - Method in TaskProcessor

@return The TaskConfig object holding the task configuration properties

getConfigEnv() - Method in ScriptBinding

The fallback session environment

getConfigProperty(def, String, String) - Method in ConfigHelper

getContainer() - Method in TaskRun

The name of a docker container where the task is supposed to run when provided

getContainerConfig() - Method in TaskRun

getContentUrl(String) - Method in BitbucketRepositoryProvider

getContentUrl(String) - Method in GithubRepositoryProvider

{@inheritDoc}

getContentUrl(String) - Method in GitlabRepositoryProvider

{@inheritDoc}

getContentUrl(String) - Method in LocalRepositoryProvider

getContentUrl(String) - Method in RepositoryProvider

The hub service API rul to access a content in the remote repository e.g. https://api.github.com/repos/nextflow-io/hello/contents/my/file

getCount() - Method in AbstractSplitter

@return The number of entry of which each chunk is made up

getCpus() - Method in TaskConfig

getCreateUser() - Method in LaunchConfig

getCurrentRevision() - Method in AssetManager

@return The symbolic name of the current revision i.e. the current checked out branch or tag

getCurrentRevisionAndName() - Method in AssetManager

getDag() - Method in Session

getDefaultBranch() - Method in AssetManager

getDefaultBranch() - Method in GitlabRepositoryProvider

getDefaultDriverName() - Method in CloudDriverFactory

@return The first and only cloud driver name or null otherwise

getDescription() - Method in AssetManager

getDescription() - Method in CmdFs.CmdCat

getDescription() - Method in CmdFs.CmdCopy

getDescription() - Method in CmdFs.CmdList

getDescription() - Method in CmdFs.CmdMove

getDescription() - Method in CmdFs.CmdRemove

getDescription() - Method in CmdFs.SubCmd

getDetailMessage(Throwable) - Method in LoggerHelper

getDirectives(TaskRun, List<String>) - Method in AbstractGridExecutor

@param task The current task object

getDirectives(TaskRun, List<String>) - Method in CirrusExecutor

getDirectives(TaskRun, List<String>) - Method in CondorExecutor

getDirectives(TaskRun, List<String>) - Method in CrgExecutor

The jobs directives used for the job submission

getDirectives(TaskRun, List<String>) - Method in KubernetesExecutor

getDirectives(TaskRun, List<String>) - Method in LsfExecutor

Gets the directives to submit the specified task to the cluster for execution

getDirectives(TaskRun, List<String>) - Method in NqsiiExecutor

Gets the directives to submit the specified task to the cluster for execution

getDirectives(TaskRun, List<String>) - Method in PbsExecutor

Gets the directives to submit the specified task to the cluster for execution

getDirectives(TaskRun, List<String>) - Method in SgeExecutor

Gets the directives to submit the specified task to the cluster for execution

getDirectives(TaskRun, List<String>) - Method in SlurmExecutor

Gets the directives to submit the specified task to the cluster for execution

getDirectivesText(TaskRun) - Method in CondorExecutor

getDisk() - Method in TaskConfig

getDispatcher() - Method in Session

@return The session TaskDispatcher

getDispatcher() - Method in TaskPollingMonitor

@return The current TaskDispatcher instance

getDockerPull() - Method in LaunchConfig

getDomain() - Method in GitUrl

Returns:

The URL domain e.g. given the URL https://gitlab.com/pditommaso/hello.git the string gitlab.com is return.

getDomain() - Method in ProviderConfig

Returns:

Remote server name e.g.

getDriver(String, Map) - Method in CloudDriverFactory

Get and instance of a concrete CloudDriver by the given driver name

getDriverName() - Method in CloudConfig

getDriverNames() - Method in CloudDriverFactory

@return The list of name of available drivers

getDumpHashes() - Method in Session

getEcho() - Method in TaskConfig

getEnabled() - Method in CloudConfig.Autoscale

getEndpoint() - Method in ProviderConfig

Returns:

The API root endpoint url e.g.

getEndpointUrl() - Method in BitbucketRepositoryProvider

getEndpointUrl() - Method in GithubRepositoryProvider

{@inheritDoc}

getEndpointUrl() - Method in GitlabRepositoryProvider

getEndpointUrl() - Method in LocalRepositoryProvider

getEndpointUrl() - Method in RepositoryProvider

The hub service API url to access the remote repository e.g. https://api.github.com/repos/nextflow-io/hello

getEngine() - Method in ContainerConfig

getEnvExports() - Method in SingularityBuilder

getEnvironment() - Method in ClusterConfig

getEnvironment() - Method in ComposedConfigSlurper

getError() - Method in Session

getErrorCount() - Method in TaskConfig

getErrorStrategy() - Method in TaskConfig

getExecConfigProp(String, String, Object, Map) - Method in Session

getExecService() - Method in Session

getExitReadTimeout(String, Duration) - Method in Session

Determines how long the executors waits before return an error status when a process is terminated but the exit file does not exist or it is empty.

getFault() - Method in Session

getFilePattern(Map) - Method in FileInParam

getFilePatterns(Map, Path) - Method in FileOutParam

getFiles() - Method in SimpleFileCollector

getFmtStr(String, String) - Method in TraceRecord

Get a trace field value and apply a conversion rule to it

getFollowLinks() - Method in FileOutParam

getFormat() - Method in GraphObserver

getGit() - Method in AssetManager

getGitConfigRemoteDomain() - Method in AssetManager

getGitConfigRemoteUrl() - Method in AssetManager

getGitRepositoryUrl() - Method in AssetManager

getGlob() - Method in FileOutParam

getGuard(String, boolean) - Method in TaskConfig

Get a closure guard condition and evaluate to a boolean result

getHashLog() - Method in TaskRun

Given an HashCode instance renders only the first 8 characters using the format showed below:

          2f/0075a6
     

getHashMode() - Method in ProcessConfig

getHeaders(TaskRun) - Method in AbstractGridExecutor

Defines the jobs directive headers

getHeaders(TaskRun) - Method in NqsiiExecutor

getHeaders(TaskRun) - Method in PbsExecutor

getHeaderToken() - Method in AbstractGridExecutor

@return String used to declare job directives in the job script wrapper

getHeaderToken() - Method in CirrusExecutor

getHeaderToken() - Method in CondorExecutor

getHeaderToken() - Method in KubernetesExecutor

getHeaderToken() - Method in LsfExecutor

getHeaderToken() - Method in NqsiiExecutor

getHeaderToken() - Method in PbsExecutor

getHeaderToken() - Method in SgeExecutor

getHeaderToken() - Method in SlurmExecutor

getHidden() - Method in FileOutParam

getHolder() - Method in TaskContext

@return The inner map holding the process variables

getHomePage() - Method in AssetManager

getHub() - Method in AssetManager

getHubPassword() - Method in HubOptions

Return the password provided on the command line or stop allowing the user to enter it on the console

getHubUser() - Method in HubOptions

getId() - Method in TaskProcessor

@return The processor unique id

getIdleTimeout() - Method in CloudConfig.Autoscale

getImageId() - Method in LaunchConfig

getInChannel() - Method in BaseInParam

@return The input channel instance used by this parameter to receive the process inputs

getInChannel() - Method in InParam

getIncludeInputs() - Method in FileOutParam

getIndex() - Method in OutParam

getInfo(int, boolean) - Method in CmdInfo

@return A string containing some system runtime information

getInner() - Method in EachInParam

getInputEnvironment() - Method in TaskRun

@return A map containing the task environment defined as input declaration by this task

getInputFiles() - Method in TaskRun

getInputFilesMap() - Method in TaskRun

@return A map object containing all the task input files as pairs

getInputs() - Method in CombineOp

getInputs() - Method in ProcessConfig

Type shortcut to #configProperties.inputs

getInputsByType(Class<T>) - Method in TaskRun

Get the map of *input* objects by the given InParam type

getInstanceStorageDevice() - Method in LaunchConfig

getInstanceStorageMount() - Method in LaunchConfig

getInstanceType(String) - Method in AmazonPriceReader

getInstanceType() - Method in LaunchConfig

getInto() - Method in AbstractSplitter

Returns:

The target object that receives the splitted chunks.

getJobNameFor(TaskRun) - Method in AbstractGridExecutor

Given a task returns a *clean* name used to submit the job to the grid engine.

getJobNameFor(TaskRun) - Method in CirrusExecutor

getJobNameFor(TaskRun) - Method in NqsiiExecutor

getJobNameFor(TaskRun) - Method in PbsExecutor

getKeyFile() - Method in CloudConfig

getKeyHash() - Method in LaunchConfig

getKeyName() - Method in LaunchConfig

getKillCommand() - Method in AbstractGridExecutor

The command to be used to kill a grid job

getKillCommand() - Method in CirrusExecutor

getKillCommand() - Method in CondorExecutor

getKillCommand() - Method in ContainerBuilder

getKillCommand() - Method in DockerBuilder

@return The command string to kill a running container

getKillCommand() - Method in KubernetesExecutor

getKillCommand() - Method in LsfExecutor

getKillCommand() - Method in NqsiiExecutor

getKillCommand() - Method in PbsExecutor

getKillCommand() - Method in SgeExecutor

getKillCommand() - Method in SlurmExecutor

getLast() - Method in HistoryFile

getLauncher() - Method in CmdBase

getLibDir() - Method in Session

getLocalInstanceId() - Method in AmazonCloudDriver

getLocalInstanceId() - Method in CloudDriver

Retrieve the instance id of the local node.

getLocalPath() - Method in AssetManager

getLocalTerminationNotice() - Method in AmazonCloudDriver

see https://aws.amazon.com/blogs/aws/new-ec2-spot-instance-termination-notices/ http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/spot-interruptions.html

getLocalTerminationNotice() - Method in CloudDriver

Retrieve a termination notice for spot/preemptive instance if available This method is meant to be invoked by a cloud VM which can be retired by the cloud provider

getMainBranch() - Method in BitbucketRepositoryProvider

getMainScriptFile() - Method in AssetManager

getMainScriptName() - Method in AssetManager

getMaxDepth() - Method in FileOutParam

getMaxErrors() - Method in TaskConfig

getMaximumNumberOfParameters() - Method in TaskClosure

getMaxInstances() - Method in CloudConfig.Autoscale

getMaxRetries() - Method in TaskConfig

getMemory() - Method in TaskConfig

getMinInstances() - Method in CloudConfig.Autoscale

getMode() - Method in BaseOutParam

getMode() - Method in CloudConfig.Nextflow

getMode() - Method in OutParam

getModule() - Method in TaskConfig

getMonitor(def) - Method in TaskDispatcher

Get the monitor associated to the executor type or instance

getMonitorDumpInterval(String, Duration) - Method in Session

Determines how often the executor status is written in the application log file

getName() - Method in BaseInParam

@return The parameter name

getName() - Method in BaseOutParam

getName() - Method in BitbucketRepositoryProvider

{@inheritDoc}

getName() - Method in CmdBase

getName() - Method in CmdClean

@return The name of this command clean

getName() - Method in CmdClone

getName() - Method in CmdCloud

Returns:

The command name i.e.

getName() - Method in CmdCloud.CreateCluster

getName() - Method in CmdCloud.JoinCluster

getName() - Method in CmdCloud.ListNodes

getName() - Method in CmdCloud.Shutdown

getName() - Method in CmdCloud.SpotPrices

getName() - Method in CmdCloud.SubCmd

getName() - Method in CmdConfig

getName() - Method in CmdDrop

getName() - Method in CmdFs

getName() - Method in CmdFs.CmdCat

getName() - Method in CmdFs.CmdCopy

getName() - Method in CmdFs.CmdList

getName() - Method in CmdFs.CmdMove

getName() - Method in CmdFs.CmdRemove

getName() - Method in CmdFs.SubCmd

getName() - Method in CmdHelp

getName() - Method in CmdHistory

getName() - Method in CmdInfo

getName() - Method in CmdList

getName() - Method in CmdLog

getName() - Method in CmdLs

getName() - Method in CmdNode

getName() - Method in CmdPull

getName() - Method in CmdRun

getName() - Method in CmdSelfUpdate

getName() - Method in CmdView

getName() - Method in EachInParam

getName() - Method in FileInParam

getName() - Method in FileOutParam

Override the default to allow null as a value name @return

getName() - Method in GithubRepositoryProvider

{@inheritDoc}

getName() - Method in GitlabRepositoryProvider

getName() - Method in GraphObserver

getName() - Method in InParam

getName() - Method in LocalRepositoryProvider

getName() - Method in OutParam

@return The parameter name getter

getName() - Method in ProviderConfig

@return The provider name as defined in the configuration file

getName() - Method in RepositoryProvider

@return The name of the source hub service e.g. github or bitbucket

getName() - Method in SetInParam

getName() - Method in SetOutParam

getName() - Method in StdInParam

getName() - Method in TaskProcessor

@return The processor name

getName() - Method in TaskRun

getName() - Method in ValueOutParam

getNames() - Method in InputsList

getNames() - Method in OutputsList

getNetworkInterfaceAddresses() - Method in ClusterConfig

Get the network interface IP addresses.

getNextflow() - Method in LaunchConfig

getNormalizedArgs() - Method in Launcher

getOperator() - Method in TaskProcessor

@return The DataflowOperator underlying this process

getOperatorName() - Method in AbstractSplitter

@return A string representing the operator invoking the splitter

getOptional() - Method in FileOutParam

getOptions() - Method in CloudConfig.Nextflow

getOptions() - Method in Launcher

getOrCreate(String) - Method in PathTrie

Get or create a not for the given path item.

getOrCreateAttribute(K, Closure<V>) - Method in CascadingConfig

getOrCreateMonitor(Class<? extends Executor>, Closure<TaskMonitor>) - Method in TaskDispatcher

Get an instance of TaskMonitor in the #monitors map, when the map contains no value for the specified executor invoke the closure in order to create a new TaskMonitor object, add it to the map and return it.

getOutChannel() - Method in BaseOutParam

getOutChannel() - Method in OutParam

@return The output channel instance

getOutChannels() - Method in BaseOutParam

getOutChannels() - Method in OutParam

getOutputFilesNames() - Method in TaskRun

Look at the nextflow.script.FileOutParam which name is the expected output name

getOutputs() - Method in IntoOp

getOutputs() - Method in ProcessConfig

Type shortcut to #configProperties.outputs

getOutputs() - Method in TapOp

@return A list holding the output channels of the `tap` operator

getOutputsByType(Class<T>) - Method in TaskRun

Get the map of *output* objects by the given InParam type

getOwnerScript() - Method in TaskProcessor

@return The BaseScript object which represents pipeline script

getParameterTypes() - Method in TaskClosure

getParent() - Method in ScriptFile

@return Directory where the main script file is stored

getParsedParams() - Method in CmdRun

getPassword() - Method in ProviderConfig

getPassword() - Method in RepositoryProvider

getPath() - Method in ProviderConfig

getPlatform() - Method in ProviderConfig

Returns:

The provider identifier e.g.

getPollInterval(String, Duration) - Method in Session

Determines how often a poll occurs to check for a process termination

getPoolSize() - Method in Session

@return The session max number of thread allowed

getPrivateKeyFile() - Method in CloudConfig

getProcessEnvironment() - Method in TaskProcessor

@return The map holding the shell environment variables for the task to be executed

getProject() - Method in AssetManager

getProject() - Method in GitUrl

@return The repository qualified name e.g. given the project repository https://github.com/cbcrg/piper-nf.git returns the string cbcrg/piper-nf.

getProjectName() - Method in GitlabRepositoryProvider

getProperty(String) - Method in ProcessConfig

getProperty(String) - Method in TaskConfig

getProperty(String) - Method in TaskContext

getProtocol() - Method in GitUrl

Returns:

The url protocol e.g. http, https, git, ssh or file.

getPublishDir() - Method in TaskConfig

getPull() - Method in CloudConfig.Nextflow

getQueueSize(String, int) - Method in Session

Defines the number of tasks the executor will handle in a parallel manner

getQueueStatInterval(String, Duration) - Method in Session

Determines how often the queue status is fetched from the cluster system.

getQueueStatus(def) - Method in AbstractGridExecutor

@return The status for all the scheduled and running jobs

getRecordFields() - Method in AbstractSplitter

@return The fields to be included in each parsed record

getRecordMode() - Method in AbstractSplitter

@return Whenever each split is parsed to a record object or a chunk in the native format i.e. text line(s) or bytes

getRemoveCommand() - Method in ContainerBuilder

getRemoveCommand() - Method in DockerBuilder

@return The command string to remove a container

getRepositoryUrl() - Method in AssetManager

getRepositoryUrl() - Method in BitbucketRepositoryProvider

getRepositoryUrl() - Method in GithubRepositoryProvider

{@inheritDoc}

getRepositoryUrl() - Method in GitlabRepositoryProvider

{@inheritDoc}

getRepositoryUrl() - Method in LocalRepositoryProvider

getRepositoryUrl() - Method in RepositoryProvider

@return The project home page e.g. https://github.com/nextflow-io/hello

getResult() - Method in ScriptRunner

@return The result produced by the script execution

getRetryCount() - Method in TaskConfig

getRevision() - Method in ScriptFile

@return Repository tag or branch

getRevisions(int) - Method in AssetManager

Returns:

A list of existing branches and tags names.

getRndTip() - Method in TaskProcessor

Display a random tip at the bottom of the error report

getRole() - Method in CloudConfig.Autoscale

getRole() - Method in LaunchConfig

getRooDeviceMapping(String) - Method in AmazonCloudDriver

getRunCommand() - Method in ContainerBuilder

getRunCommand() - Method in DockerBuilder

@return The command string to run a container from Docker image

getRunCommand() - Method in ShifterBuilder

getRunCommand() - Method in SingularityBuilder

getRunCommand() - Method in UdockerBuilder

getRunningQueue() - Method in TaskPollingMonitor

@return The current runningQueue instance

getScope() - Method in ClusterConfig

getScratch() - Method in TaskRun

getScratchDirectoryCommand() - Method in BashWrapperBuilder

@return The bash script fragment to change to the 'scratch' directory if it has been specified in the task configuration

getScript() - Method in TaskContext

@return The script instance to which this map reference i.e. the main script object

getScript() - Method in TaskRun

getScriptFile() - Method in AssetManager

getScriptFile(String) - Method in CmdRun

getScriptFromStream(InputStream, String) - Method in CmdRun

getScriptId() - Method in ScriptFile

getScriptObj() - Method in ScriptRunner

@return The interpreted script object

getScriptType() - Method in TaskProcessor

Define the type of script hold by the #code property

getScriptVar(String) - Method in BaseParam

getSecurityGroup() - Method in LaunchConfig

getSecurityGroups() - Method in LaunchConfig

getSeparatorChar() - Method in FileOutParam

getServer() - Method in ProviderConfig

Returns:

Remote server including protocol and eventually port number e.g.

getSession() - Method in ScriptRunner

getSession() - Method in TaskProcessor

@return The current Session instance

getSharedStorageId() - Method in LaunchConfig

getSharedStorageMount() - Method in LaunchConfig

getShell() - Method in TaskConfig

getShortcut() - Method in CmdCloud.CreateCluster

getShortcut() - Method in CmdCloud.JoinCluster

getShortcut() - Method in CmdCloud.ListNodes

getShortcut() - Method in CmdCloud.Shutdown

getShortcut() - Method in CmdCloud.SpotPrices

getShortcut() - Method in CmdCloud.SubCmd

getSource() - Method in FailedGuardException

getSource() - Method in TaskClosure

getSourceUnit() - Method in NextflowDSLImpl.GStringToLazyVisitor

getSourceUnit() - Method in NextflowDSLImpl.VariableVisitor

getSpotPrice() - Method in LaunchConfig

getSshCommand(CloudConfig, String) - Method in CmdCloud

A string describing the SSH command to login into the cluster master instance

getStagedInputs() - Method in TaskRun

Return the list of all input files staged as inputs by this task execution

getStageInputFilesScript() - Method in ScriptFileCopyStrategy

@return A BASH snippet included in the wrapper script that stages the task input files

getStageInputFilesScript() - Method in SimpleFileCopyStrategy

Given a map of the input file parameters with respective values, create the BASH script to stage them into the task working space

getStarvingTimeout() - Method in CloudConfig.Autoscale

getStatsEnabled() - Method in Session

getStatusString() - Method in CachedTaskHandler

getStatusString() - Method in TaskHandler

getStderr() - Method in TaskRun

getStdout() - Method in TaskRun

@return The task produced stdout result as string

getStoreDir() - Method in TaskConfig

getSubmitCommandLine(TaskRun, Path) - Method in AbstractGridExecutor

Build up the platform native command line used to submit the job wrapper execution request to the underlying grid, e.g.

getSubmitCommandLine(TaskRun, Path) - Method in CirrusExecutor

getSubmitCommandLine(TaskRun, Path) - Method in CondorExecutor

getSubmitCommandLine(TaskRun, Path) - Method in KubernetesExecutor

Define the Kubernates job execution command line

getSubmitCommandLine(TaskRun, Path) - Method in LsfExecutor

The command line to submit this job

getSubmitCommandLine(TaskRun, Path) - Method in NqsiiExecutor

getSubmitCommandLine(TaskRun, Path) - Method in PbsExecutor

The command line to submit this job

getSubmitCommandLine(TaskRun, Path) - Method in SgeExecutor

getSubmitCommandLine(TaskRun, Path) - Method in SlurmExecutor

The command line to submit this job

getSubnetId() - Method in LaunchConfig

getSysEnv() - Method in ScriptBinding

getTargetDir() - Method in TaskRun

getTargetObj() - Method in AbstractSplitter

@return The splitter raw target object

getTask() - Method in TaskHandler

The task managed by this handler

getTaskBody() - Method in TaskProcessor

@return The user provided script block

getTaskEntry(HashCode, TaskProcessor) - Method in CacheDB

Retrieve a task runtime information from the cache DB

getTaskGlobalVars(Set<String>, Binding, Map) - Method in TaskProcessor

@param variableNames The collection of variables referenced in the task script

getTaskId() - Method in TraceRecord

getTempDir() - Method in FileCollector

Retrieve the collector temporary folder i.e. working directory.

getTerminateWhenIdle() - Method in CloudConfig.Autoscale

getTerminationPolicy() - Method in CloudConfig.Autoscale

getText() - Method in ScriptFile

@return Main script file content as a text string

getTime() - Method in TaskConfig

getToken() - Method in ProviderConfig

getTrace() - Method in CloudConfig.Nextflow

getTraceRecord() - Method in CachedTaskHandler

getTraceRecord() - Method in GridTaskHandler

@return An TraceRecord instance holding task runtime information

getTraceRecord() - Method in LocalTaskHandler

@return An TraceRecord instance holding task runtime information

getTraceRecord() - Method in TaskHandler

@return An TraceRecord instance holding task runtime information

getType() - Method in FileOutParam

getTypeName() - Method in BaseInParam

getTypeName() - Method in DefaultInParam

getTypeName() - Method in EachInParam

getTypeName() - Method in EnvInParam

getTypeName() - Method in FileInParam

getTypeName() - Method in SetInParam

getTypeName() - Method in StdInParam

getTypeName() - Method in ValueInParam

getUniqueId() - Method in Session

@return The current session java.util.UUID

getUnstageOutputFilesScript() - Method in CirrusFileCopyStrategy

{@inheritDoc}

getUnstageOutputFilesScript() - Method in S3FileCopyStrategy

{@inheritDoc}

getUnstageOutputFilesScript() - Method in ScriptFileCopyStrategy

@return A BASH snippet included in the wrapper script that un-stages the task output files

getUnstageOutputFilesScript() - Method in SimpleFileCopyStrategy

Creates the script to unstage the result output files from the scratch directory to the shared working directory

getUser() - Method in GitUrl

@return The user name eventually specified in the url string

getUser() - Method in ProviderConfig

getUser() - Method in RepositoryProvider

getUserName() - Method in LaunchConfig

getValidExitStatus() - Method in TaskConfig

getValNames() - Method in TaskBody

Returns:

The set of variable and properties referenced in the user script.

getValue(long) - Method in SortFileCollector.IndexSort

getVariable(String) - Method in ScriptBinding

Try to get a value in the current bindings, if does not exist try to fallback on the session environment.

getVariableNames() - Method in TaskContext

Returns:

The set of variable and properties referenced in the user script.

getVersion() - Method in CloudConfig.Nextflow

getVersion(boolean) - Method in Launcher

Print the application version number

getVertex() - Method in Trie

getWorkDir() - Method in TraceRecord

getWorkDirStr() - Method in TaskRun

GithubRepositoryProvider - Class in nextflow.scm

Implements a repository provider for GitHub service

GithubRepositoryProvider(String, ProviderConfig) - Constructor in GithubRepositoryProvider

GitlabRepositoryProvider - Class in nextflow.scm

Implements a repository provider for GitHub service

GitlabRepositoryProvider(String, ProviderConfig) - Constructor in GitlabRepositoryProvider

GitUrl - Class in nextflow.scm

Models Git URL

GitUrl(String) - Constructor in GitUrl

Creates a Git URL object parsing the URL string

glob - Field in FileOutParam

GraphObserver - Class in nextflow.trace

Render the DAG document on pipeline completion using the format specified by the user

GraphObserver(Path) - Constructor in GraphObserver

GraphvizRenderer - Class in nextflow.dag

@author Paolo Di Tommaso

GraphvizRenderer(String, String) - Constructor in GraphvizRenderer

grengine - Field in TaskProcessor

Groovy engine used to evaluate dynamic code

GridTaskHandler - Class in nextflow.executor

Handles a job execution in the underlying grid platform

GridTaskHandler(TaskRun, AbstractGridExecutor) - Constructor in GridTaskHandler

group - Field in TaskProcessor

Gpars thread pool

groupBy(DataflowReadChannel, def) - Method in DataflowExtensions

Sorts all collection members into groups determined by the supplied mapping closure

groupTuple(DataflowReadChannel, Map) - Method in DataflowExtensions

GroupTupleOp - Class in nextflow.extension

Implements DataflowExtensions.groupTuple operator logic

GroupTupleOp(Map, DataflowReadChannel) - Constructor in GroupTupleOp

GStringSerializer - Class in nextflow.util

Serializer / de-serializer for Groovy GString

guessHubProviderFromGitConfig() - Method in AssetManager

H

handleException(TaskHandler, Throwable) - Method in TaskPollingMonitor

handleException(Throwable, TaskRun) - Method in TaskProcessor

Handles an error raised during the processor execution

hasCacheableValues() - Method in TaskRun

Check whenever there are values to be cached

hasChunk() - Method in CharSequenceCollector

hasChunk() - Method in CollectorStrategy

@return true if at least an item as been added

hasChunk() - Method in ObjectListCollector

hasChunk() - Method in TextFileCollector

hasContainerDirective(def) - Method in ConfigBuilder

Verify that configuration for process contains at last one `container` directive

hasCredentials() - Method in RepositoryProvider

hasEachParams - Field in TaskProcessor

hashCode() - Method in TaskId

hashCode() - Method in TraceRecord

hasPublicAddress() - Method in CloudInstance

hasVariable(String) - Method in ScriptBinding

Override variable existence

HexIdentity - Class in nextflow.util

Hexadecimal identify value class

hidden(boolean) - Method in FileOutParam

HistoryFile - Class in nextflow.util

Manages the history file containing the last 1000 executed commands

HistoryFile.Record - Class in nextflow.util

HistoryFile.Record() - Constructor in HistoryFile.Record

HistoryFile(Path) - Constructor in HistoryFile

holder - Field in BaseParam

HubOptions - Trait in nextflow.cli

Defines the command line parameters for command that need to interact with a pipeline service hub i.e.

I

ifEmpty(DataflowReadChannel, def) - Method in DataflowExtensions

Empty the specified value only if the source channel to which is applied is empty i.e. do not emit any value.

ignoreNewLine - Field in StringSplitter

IllegalConfigException - Class in nextflow.exception

Exception thrown when container configuration options are invalid

IllegalDirectiveException - Class in nextflow.exception

Exception throw

IllegalFileException - Class in nextflow.exception

Exception thrown when a process tries to output a file out located out of it's working directory

image - Field in ContainerBuilder

includeConfig(def) - Method in ComposedConfigScript

Implements the config file include

includeHidden - Field in FileOutParam

When true star wildcard (*) matches hidden files (files starting with a dot char) By default it does not, coherently with linux bash rule

includeInputs - Field in FileOutParam

When true file pattern includes input files as well as output files.

incTaskEntry(HashCode) - Method in CacheDB

indexCount - Field in TaskProcessor

Unique task index number (run)

init() - Method in AbstractGridExecutor

Initialize the executor class

init() - Method in BaseParam

Initialize the parameter fields if needed

init() - Method in CacheBase

init() - Method in CmdLog

init() - Method in Executor

Allows to post-initialize the executor

init() - Method in Launcher

init(Path) - Method in Session

Initialize the session workDir, libDir, baseDir and scriptName variables

InParam - Interface in nextflow.script

Basic interface for *all* input parameters

InputsList - Class in nextflow.script

Container to hold all process outputs

inputValToChannel(def) - Method in BaseParam

inputValToChannel(def) - Method in EachInParam

InstantiationStrategy - Class in nextflow.util

interval(String, Closure) - Method in Channel

Creates a channel emitting a sequence of value given by the closure and spaced by a given time interval.

into - Field in AbstractSplitter

into(TokenVar) - Method in BaseOutParam

into(DataflowReadChannel, Closure) - Method in DataflowExtensions

Forward source dataflow channel *into* one or more dataflow channels.

into(def) - Method in OutParam

Defines the channel to which bind the output(s) in the script context

intoObj - Field in BaseOutParam

IntoOp - Class in nextflow.extension

Implements the DataflowExtensions.into operators logic

IntoOp(DataflowReadChannel, Closure) - Constructor in IntoOp

intValue() - Method in TaskId

invoke(String) - Method in RepositoryProvider

Invoke the API request specified

invokeAndParseResponse(String) - Method in RepositoryProvider

Invoke the API request specified and parse the JSON response

invokeMethod(String, Object) - Method in TaskContext

invokeOnError(def) - Method in WorkflowMetadata

invokeTask(def) - Method in TaskProcessor

The processor execution body

isAborted() - Method in Session

isAbsoluteDockerName(String) - Method in DockerBuilder

isCacheable() - Method in ProcessConfig

isCacheable() - Method in TaskProcessor

Whenever the process can be cached

isCached() - Method in TraceRecord

isCancelled() - Method in Session

isClean() - Method in AssetManager

@return true if no differences exist between the working-tree, the index, and the current HEAD, false if differences do exist

isCloudCluster() - Method in ClusterConfig

isCollectorEnabled() - Method in AbstractTextSplitter

isCompleted() - Method in Barrier

@return true when all parties have arrived

isCompleted() - Method in TaskHandler

isContainerExecutable() - Method in TaskRun

@return {@true} when the process runs an *executable* container

isDaemon() - Method in Launcher

isDockerEnabled() - Method in TaskRun

@return {@true} when the process must run within a container and the docker engine is enabled

isDynamic() - Method in FileOutParam

@return true when the file name is parametric i.e contains a variable name to be resolved, false otherwise

isEmpty() - Method in CascadingConfig

isEmpty() - Method in DAG

isEmpty() - Method in SimpleFileCollector

isEnabled() - Method in ContainerConfig

isLegacy() - Method in ContainerConfig

isLocal() - Method in AssetManager

isNew() - Method in TaskHandler

isNormalized(PropertyExpression) - Method in NextflowDSLImpl.VariableVisitor

isPerJobMemLimit() - Method in LsfExecutor

isProcessorActive(DataflowProcessor) - Method in DataflowHelper

Check if a DataflowProcessor is active

isRunnable() - Method in AssetManager

@return true when the local project path exists and contains at least the default script file (i.e. main.nf) or the nextflow manifest file (i.e. nextflow.config)

isRunning() - Method in TaskHandler

isSpot() - Method in LaunchConfig

isSubmitted() - Method in TaskHandler

isSuccess() - Method in Session

isSuccess(def) - Method in TaskRun

isTerminated() - Method in Session

isTriggeringEvent(File, E) - Method in LoggerHelper.RollOnStartupPolicy

isTrueOrMap(def) - Method in AbstractSplitter

@param value An object to check

isTypeSupported(ScriptType, def) - Method in ProcessFactory

isWithinMethod(MethodCallExpression, String) - Method in NextflowDSLImpl

J

just(def) - Method in Channel

Convert an object into a *channel* variable that emits that object

K

keySet() - Method in TraceRecord

kill() - Method in BatchCleanup

Group together jobs for the same executor and kill them in bunch of a given size

kill() - Method in CachedTaskHandler

kill() - Method in GridTaskHandler

kill() - Method in LocalTaskHandler

Force the submitted job to quit

kill() - Method in NativeTaskHandler

kill() - Method in NopeTaskHandler

kill() - Method in TaskHandler

Force the submitted job to quit

killTask(def) - Method in AbstractGridExecutor

Kill a grid job

killTaskCommand(def) - Method in AbstractGridExecutor

The command to be used to kill a grid job

kryo() - Method in KryoHelper

@return A new instance Kryo instance

KryoHelper - Class in nextflow.util

Helper class to get a Kryo object ready to be used

KubernetesExecutor - Class in nextflow.executor

Kubernetes executor

KubernetesExecutor.KubernetesWrapperBuilder - Class in nextflow.executor

Extends BashWrapperBuilder to handle Kubernetes job description YAML file

KubernetesExecutor.KubernetesWrapperBuilder(TaskBean) - Constructor in KubernetesExecutor.KubernetesWrapperBuilder

KubernetesExecutor.YamlBuilder - Class in nextflow.executor

Kubernetes job YAML descriptor build helper

L

labelString(TraceRecord) - Method in TimelineObserver

last(DataflowReadChannel<V>) - Method in DataflowExtensions

The last operator creates a channel that only returns the last item emitted by the source channel

launch(Map) - Method in DaemonLauncher

LaunchConfig - Class in nextflow.cloud

Model a cloud instance launch configuration properties

LaunchConfig(Map, CascadingConfig<String, Object>) - Constructor in LaunchConfig

launchDaemon(String) - Method in CmdNode

Launch the daemon service

Launcher - Class in nextflow.cli

Main application entry point.

LAUNCHER - Field in DripMain

Launcher() - Constructor in Launcher

Create a launcher object and parse the command line parameters

launchInstances(int, LaunchConfig) - Method in AmazonCloudDriver

launchInstances(int, LaunchConfig) - Method in CloudDriver

Launch cloud instances given the specified configuration

lazyInit() - Method in BaseInParam

Lazy parameter initializer.

lazyInit() - Method in BaseOutParam

lazyInit() - Method in BaseParam

Lazy initializer

lazyLibDir() - Method in RemoteSession

@return The list of folder containing the unzip libraries

LazyMap - Class in nextflow.processor

A map that resolve closure and gstring in a lazy manner

LazyMap(Map<String, Object>) - Constructor in LazyMap

LevelDbSort - Class in nextflow.sort

Level-DB based big sort

limit - Field in AbstractSplitter

list() - Method in AbstractSplitter

@return Split the target objects and return a list containing all chunks

list() - Method in AssetManager

@return The list of available pipelines

list() - Method in SplitterStrategy

listIds() - Method in CacheBase

listPrivateIPs(String) - Method in AmazonCloudDriver

listPrivateIPs(String) - Method in CloudDriver

Retrieve the private IPs of all node in the cluster with the specified name

loadDaemonByClass(String) - Method in CmdNode

Load a class implementing the DaemonLauncher interface by the specified class name

loadDaemonByName(String) - Method in CmdNode

Load a DaemonLauncher instance of the its *friendly* name i.e. the name provided by using the ServiceName annotation on the daemon class definition

loadDaemonFirst() - Method in CmdNode

@return The first available instance of a class implementing DaemonLauncher

loadDrivers() - Method in CloudDriverFactory

@return The map of cloud drivers available on the current class path

loadExecutorClass(String) - Method in ProcessFactory

LocalExecutor - Class in nextflow.executor

Executes the specified task on the locally exploiting the underlying Java thread pool

LocalPollingMonitor - Class in nextflow.processor

Task polling monitor specialized for local execution.

LocalPollingMonitor(Map) - Constructor in LocalPollingMonitor

Create the task polling monitor with the provided named parameters object.

LocalRepositoryProvider - Class in nextflow.scm

Local storage asset provider

LocalRepositoryProvider(String, ProviderConfig) - Constructor in LocalRepositoryProvider

LocalTaskHandler - Class in nextflow.executor

A process wrapper adding the ability to access to the Posix PID and the hasExited flag

LocalTaskHandler(TaskRun, LocalExecutor) - Constructor in LocalTaskHandler

log - Field in Nextflow

LoggerHelper - Class in nextflow.util

Helper class to setup the logging subsystem

LoggerHelper.ConsoleLoggerFilter - Class in nextflow.util

LoggerHelper.ConsoleLoggerFilter(Map<String, Level>) - Constructor in LoggerHelper.ConsoleLoggerFilter

LoggerHelper.PrettyConsoleLayout - Class in nextflow.util

LoggerHelper.RollOnStartupPolicy - Class in nextflow.util

Trigger a new log file on application start-up

LoggerHelper(CliOptions) - Constructor in LoggerHelper

longest() - Method in PathTrie

Retrieve the list of the longest paths.

longest() - Method in Trie

longValue() - Method in TaskId

LsfExecutor - Class in nextflow.executor

Processor for LSF resource manager (DRAFT)

M

main(String) - Method in DripMain

main(String) - Method in Launcher

Hey ..

MAIN_PACKAGE - Field in Const

The application main package name

makeConfig(String) - Method in CmdCloud

Creates the CloudConfig object with the given command line options

makeCopy() - Method in TaskRun

makeEnv(def, StringBuilder) - Method in ContainerBuilder

Get the env command line option for the give environment definition

makeEnv(def, StringBuilder) - Method in ShifterBuilder

Get the env command line option for the give environment definition

makeEnv(def, StringBuilder) - Method in SingularityBuilder

makeGStringLazyVisitor - Field in NextflowDSLImpl

makeHash() - Method in FileCollector

makeHash() - Method in SortFileCollector

makeTaskContextStage1(TaskRun, Map, List) - Method in TaskProcessor

makeTaskContextStage2(TaskRun, Map, int) - Method in TaskProcessor

makeTaskContextStage3(TaskRun, HashCode, Path) - Method in TaskProcessor

makeVolumes(List<Path>, StringBuilder) - Method in ContainerBuilder

Get the volumes command line options for the given list of input files

makeVolumes(List<Path>, StringBuilder) - Method in SingularityBuilder

MANIFEST_FILE_NAME - Field in AssetManager

map(DataflowReadChannel<?>, Closure<V>) - Method in DataflowExtensions

Transform the items emitted by a channel by applying a function to each of them

MapEntrySerializer - Class in nextflow.util

MapOp - Class in nextflow.extension

Implements DataflowExtensions.map operator

MapOp(DataflowReadChannel<?>, Closure) - Constructor in MapOp

markComplete() - Method in CacheableCollector

MatcherInstantiator - Class in nextflow.util

Kryo throws an IllegalAccessError when deserializing a java.util.regex.Matcher object, thus implements a custom instantiator object

max(DataflowQueue<V>, Comparator<V>) - Method in DataflowExtensions

The max operator waits until the source channel completes, and then emits the value that had the greatest value.

maxDepth - Field in FileOutParam

Maximum number of directory levels to visit (default: no limit)

mean(DataflowQueue, Closure) - Method in DataflowExtensions

memory - Field in ContainerBuilder

merge(DataflowReadChannel, List<DataflowReadChannel<Object>>, Closure<V>) - Method in DataflowExtensions

messageArrived(DataflowProcessor, DataflowReadChannel<Object>, int, Object) - Method in TaskProcessor.BaseProcessInterceptor

messageArrived(DataflowProcessor, DataflowReadChannel<Object>, int, Object) - Method in TaskProcessor.TaskProcessorInterceptor

methodMissing(String, def) - Method in BlankSeparatedList

methodMissing(String, def) - Method in ProcessConfig

min(DataflowQueue<V>, Comparator) - Method in DataflowExtensions

The min operator waits until the source channel completes, and then emits the value that had the lowest value

MissingFileException - Class in nextflow.exception

An expected result file is missing

MissingLibraryException - Class in nextflow.exception

An expected result file is missing

MissingValueException - Class in nextflow.exception

An expected result file is missing

mix(DataflowReadChannel, DataflowReadChannel) - Method in DataflowExtensions

Similar to https://github.com/Netflix/RxJava/wiki/Combining-Observables#merge

mode - Field in BaseOutParam

mode(def) - Method in SetOutParam

module(def) - Method in ProcessConfig

moduleLoad(String) - Method in BashWrapperBuilder

mounts - Field in ContainerBuilder

MultipleInputChannelException - Class in nextflow.dag

Exception thrown when the same channel is declared as input more than one time.

MultipleInputChannelException(String, Vertex, Vertex) - Constructor in MultipleInputChannelException

MultipleOutputChannelException - Class in nextflow.dag

Exception raised then the same channel is declared as output more than one time

MultipleOutputChannelException(String, Vertex, Vertex) - Constructor in MultipleOutputChannelException

N

NA - Field in TraceRecord

NAME - Field in CmdClean

NAME - Field in CmdClone

NAME - Field in CmdCloud

NAME - Field in CmdConfig

NAME - Field in CmdDrop

NAME - Field in CmdFs

NAME - Field in CmdHelp

NAME - Field in CmdHistory

NAME - Field in CmdInfo

NAME - Field in CmdList

NAME - Field in CmdLog

NAME - Field in CmdNode

NAME - Field in CmdPull

NAME - Field in CmdRun

NAME - Field in CmdView

name(def) - Method in FileInParam

Define the file name

name - Field in TaskProcessor

The processor descriptive name

NameGenerator - Class in nextflow.util

Generate a random mnemonic name

nameObj - Field in BaseOutParam

The out parameter name

NativeTaskHandler - Class in nextflow.executor

Executes a native piece of groovy code

NativeTaskHandler(TaskRun, Executor) - Constructor in NativeTaskHandler

newInputStream(Path) - Method in AbstractSplitter

Given a java.nio.file.Path return a new java.io.InputStream associated to it.

newInstance() - Method in MatcherInstantiator

newInstantiatorOf(Class) - Method in InstantiationStrategy

newObj(Class, Object) - Method in NextflowDSLImpl

Creates a new ConstructorCallExpression for the specified class and arguments specified using an open array.

newReader(Path, Charset) - Method in AbstractTextSplitter

Create a new reader object for the given path

newTaskProcessor(String, Executor, Session, BaseScript, ProcessConfig, TaskBody) - Method in ProcessFactory

Create a new task processor and initialise with the given parameters

next() - Method in CharSequenceCollector

next() - Method in CollectorStrategy

Skip to the next chunk.

next(Collection<String>) - Method in NameGenerator

next() - Method in ObjectListCollector

next() - Method in TaskId

next() - Method in TextFileCollector

Nextflow - Class in nextflow

Defines the main methods imported by default in the script scope

NextflowDSL - Annotation Type in nextflow.ast

Marker interface which to apply AST transformation to process declaration

NextflowDSLImpl - Class in nextflow.ast

Implement some syntax sugars of Nextflow DSL scripting.

NextflowDSLImpl.GStringToLazyVisitor - Class in nextflow.ast

Transform any GString to a Lazy GString i.e.

NextflowDSLImpl.GStringToLazyVisitor(SourceUnit) - Constructor in NextflowDSLImpl.GStringToLazyVisitor

NextflowDSLImpl.VariableVisitor - Class in nextflow.ast

Visit a closure and collect all referenced variable names

NextflowDSLImpl.VariableVisitor(SourceUnit) - Constructor in NextflowDSLImpl.VariableVisitor

NodeMarker - Class in nextflow.dag

Helper class to mark DAG node with the proper labels

NON_PRIMITIVE_TYPES - Field in TraceRecord

NopeExecutor - Class in nextflow.executor

Dummy executor, only for test purpose

NopeTaskHandler - Class in nextflow.executor

NopeTaskHandler(TaskRun) - Constructor in NopeTaskHandler

normalize() - Method in DAG

normalizeGlobStarPaths(List<String>) - Method in SimpleFileCopyStrategy

Normalize path that contains glob star wildcards (i.e. double star character) since they are not supported by plain BASH

normalizeImageName(String, Map) - Method in DockerBuilder

normalizeImageName(String, Map) - Method in ShifterBuilder

Normalize Shifter image name adding `docker:` prefix or `:latest` when required

normalizeImageName(String) - Method in SingularityBuilder

normalizeImageName(String) - Method in UdockerBuilder

Normalize Shifter image name adding `docker:` prefix or `:latest` when required

normalizeInputToFile(Object, String) - Method in TaskProcessor

An input file parameter can be provided with any value other than a file.

normalizeInputToFiles(Object, int) - Method in TaskProcessor

normalizeOutput() - Method in ScriptRunner

normalizeScript(String, def) - Method in TaskProcessor

Remove extra leading, trailing whitespace and newlines chars, also if the script does not start with a shebang line, add the default by using the current #shell attribute

normalizeSource(def) - Method in AbstractBinarySplitter

normalizeSource(def) - Method in AbstractSplitter

Normalise the source object to be splitted

normalizeSource(def) - Method in AbstractTextSplitter

Creates a java.io.Reader for the given object.

normalizeToStream0(def) - Method in FileCollector

Normalize values to a java.io.InputStream

normalizeToStream(def) - Method in FileCollector

notifyError(TaskHandler) - Method in Session

Notify a task failure

notifyProcessCreate(TaskProcessor) - Method in Session

notifyTaskCached(TaskHandler) - Method in Session

notifyTaskComplete(TaskHandler) - Method in Session

Notifies task termination event

notifyTaskStart(TaskHandler) - Method in Session

Notifies task start event

notifyTaskSubmit(TaskHandler) - Method in Session

Notifies that a task has been submitted

NqsiiExecutor - Class in nextflow.executor

Execute a task script by running it on the NQSII cluster

NXF_MAX_THREADS - Field in CustomPoolFactory

NXF_POOL_TYPE - Field in CustomPoolFactory

NXF_QUEUE_SIZE - Field in CustomPoolFactory

O

ObjectListCollector - Class in nextflow.splitter

A collector strategy that creates a chunks as java.util.List of objects

of(def) - Method in TaskId

ofType(Class<T>) - Method in InputsList

ofType(Class<T>) - Method in OutputsList

onComplete(Closure) - Method in WorkflowMetadata

Implements the following idiom in the pipeline script:

     workflow.onComplete {
         // do something
     }
 

onError(Closure) - Method in Session

Define the error event handler

onError(Closure) - Method in WorkflowMetadata

Implements the following idiom in the pipeline script:

     workflow.onError {
         // do something
     }
 

onException(DataflowProcessor, Throwable) - Method in TaskProcessor.TaskProcessorInterceptor

Invoked if an exception occurs.

onFlowComplete() - Method in ExtraeTraceObserver

This method is invoked when the flow is going to complete

onFlowComplete() - Method in GraphObserver

onFlowComplete() - Method in TimelineObserver

Save the pending processes and close the trace file

onFlowComplete() - Method in TraceFileObserver

Save the pending processes and close the trace file

onFlowComplete() - Method in TraceObserver

This method is invoked when the flow is going to complete

onFlowStart(Session) - Method in ExtraeTraceObserver

Initialize the Extrae sub-system.

onFlowStart(Session) - Method in GraphObserver

onFlowStart(Session) - Method in TimelineObserver

Create the trace file, in file already existing with the same name it is "rolled" to a new file

onFlowStart(Session) - Method in TraceFileObserver

Create the trace file, in file already existing with the same name it is "rolled" to a new file

onFlowStart(Session) - Method in TraceObserver

The is method is invoked when the flow is going to start

onProcessCached(TaskHandler) - Method in ExtraeTraceObserver

onProcessCached(TaskHandler) - Method in GraphObserver

onProcessCached(TaskHandler) - Method in TimelineObserver

onProcessCached(TaskHandler) - Method in TraceFileObserver

onProcessCached(TaskHandler) - Method in TraceObserver

method invoked when a task execution is skipped because a cached result is found

onProcessComplete(TaskHandler) - Method in ExtraeTraceObserver

onProcessComplete(TaskHandler) - Method in GraphObserver

onProcessComplete(TaskHandler) - Method in TimelineObserver

This method is invoked when a process run completes

onProcessComplete(TaskHandler) - Method in TraceFileObserver

This method is invoked when a process run completes

onProcessComplete(TaskHandler) - Method in TraceObserver

This method is invoked when a process run completes

onProcessCreate(TaskProcessor) - Method in ExtraeTraceObserver

onProcessCreate(TaskProcessor) - Method in GraphObserver

onProcessCreate(TaskProcessor) - Method in TimelineObserver

onProcessCreate(TaskProcessor) - Method in TraceFileObserver

onProcessCreate(TaskProcessor) - Method in TraceObserver

onProcessStart(TaskHandler) - Method in ExtraeTraceObserver

onProcessStart(TaskHandler) - Method in GraphObserver

onProcessStart(TaskHandler) - Method in TimelineObserver

This method is invoked when a process run is going to start

onProcessStart(TaskHandler) - Method in TraceFileObserver

This method is invoked when a process run is going to start

onProcessStart(TaskHandler) - Method in TraceObserver

This method is invoked when a process run is going to start

onProcessSubmit(TaskHandler) - Method in ExtraeTraceObserver

onProcessSubmit(TaskHandler) - Method in GraphObserver

onProcessSubmit(TaskHandler) - Method in TimelineObserver

This method is invoked before a process run is going to be submitted

onProcessSubmit(TaskHandler) - Method in TraceFileObserver

This method is invoked before a process run is going to be submitted

onProcessSubmit(TaskHandler) - Method in TraceObserver

This method is invoked before a process run is going to be submitted

onShutdown(Closure) - Method in Session

Register a shutdown hook to close services when the session terminates

open() - Method in CacheDB

Initialise the database structure on the underlying file system

openForRead() - Method in CacheDB

Open the database in read mode

openPorts - Field in TaskProcessor

Track the status of input ports.

operator - Field in TaskProcessor

The corresponding DataflowProcessor which will receive and manage accordingly the task inputs

operatorName - Field in AbstractSplitter

optional - Field in FileOutParam

options(Map) - Method in AbstractSplitter

Defines the splitter parameter.

options(Map) - Method in AbstractTextSplitter

options(Map) - Method in CsvSplitter

Set the splitter options by specifying a map of named parameters.

options(Map) - Method in SplitterStrategy

options(Map) - Method in StringSplitter

OutParam - Interface in nextflow.script

Model a process generic input parameter

OutParam.Mode - Interface in nextflow.script

OutputsList - Class in nextflow.script

Container to hold all process outputs

outputValToChannel(Object) - Method in BaseOutParam

Creates a channel variable in the script context

owner - Field in BaseInParam

ownerScript - Field in TaskProcessor

The script object which defines this task

P

params(Map) - Method in ContainerBuilder

params(Map) - Method in DockerBuilder

params(Map) - Method in ShifterBuilder

params(Map) - Method in SingularityBuilder

params(Map) - Method in UdockerBuilder

parent - Field in CascadingConfig

parse(String) - Method in AmazonPriceReader

Download and parse AWS price file

parse(Script, URL) - Method in ComposedConfigSlurper

Parses the passed groovy.lang.Script instance using the second argument to allow the ConfigObject to retain an reference to the original location other Groovy script

parse(String) - Method in ContainerScriptTokens

Parse a shell script retuning a triple which contains the docker image, the line on which the docker image has been defined and any environment variable eventually defined before the image definition

parse(String) - Method in HistoryFile.Record

parseFastaRecord(CharSequence, Map) - Method in FastaSplitter

Parse a CharSequence as a FASTA formatted text, retuning a Map object containing the fields as specified by the @{code record} parameter.

parseHeader(BufferedReader) - Method in CsvSplitter

parseJobId(String) - Method in AbstractGridExecutor

Given the string returned the by grid submit command, extract the process handle i.e. the grid jobId

parseJobId(String) - Method in CirrusExecutor

parseJobId(String) - Method in CondorExecutor

parseJobId(String) - Method in KubernetesExecutor

Parse the output of a `kubectl create ` to find out the job ID

parseJobId(String) - Method in LsfExecutor

Parse the string returned by the bsub command and extract the job ID string

parseJobId(String) - Method in NqsiiExecutor

Parse the string returned by the qsub command and extract the job ID string

parseJobId(String) - Method in PbsExecutor

Parse the string returned by the qsub command and extract the job ID string

parseJobId(String) - Method in SgeExecutor

Parse the string returned by the qsub command and extract the job ID string

parseJobId(String) - Method in SlurmExecutor

Parse the string returned by the sbatch command and extract the job ID string

parseQueueStatus(String) - Method in AbstractGridExecutor

Parse the command stdout produced by the command line #queueStatusCommand

parseQueueStatus(String) - Method in CirrusExecutor

parseQueueStatus(String) - Method in CondorExecutor

parseQueueStatus(String) - Method in KubernetesExecutor

parseQueueStatus(String) - Method in LsfExecutor

parseQueueStatus(String) - Method in NqsiiExecutor

parseQueueStatus(String) - Method in PbsExecutor

parseQueueStatus(String) - Method in SgeExecutor

parseQueueStatus(String) - Method in SlurmExecutor

parseScript(String, List<String>) - Method in ScriptRunner

parseTraceFile(Path) - Method in TraceRecord

Parse the trace file

parseValue(def) - Method in BasicMode

parseValue(def) - Method in ConfigHelper

PathSerializer - Class in nextflow.util

A Kryo serializer to handler a Path object

PathTrie - Class in nextflow.util

A trie data structure specialised to find the longest common paths in a given list of paths

PathTrie() - Constructor in PathTrie

PatternSerializer - Class in nextflow.util

The java.util.regex.Pattern class does not have default constructor as required by Kryo, but implements the java.io.Serializable interface, thus use the default serialization mechanism to store the pattern as a byte array

PbsExecutor - Class in nextflow.executor

Implements a executor for PBS/Torque cluster

phase(DataflowReadChannel, DataflowReadChannel, Closure) - Method in DataflowExtensions

PhaseOp - Class in nextflow.extension

Implements DataflowExtensions.phase operator logic

PhaseOp(DataflowReadChannel, DataflowReadChannel) - Constructor in PhaseOp

pipeLauncherScript() - Method in AbstractGridExecutor

Defines how script is run the by the grid-engine.

pipeLauncherScript() - Method in LsfExecutor

@return true since BSC grid requires the script to be piped to the bsub command

placeholderChar() - Method in TaskRun

pollLoop() - Method in TaskPollingMonitor

Implements the polling strategy

prettyPrint() - Method in CloudConfig

Render the cloud config in a human readable way

print(DataflowReadChannel<?>, Closure) - Method in DataflowExtensions

Print the channel content to the console standard output

print() - Method in HistoryFile

printCommands(List<CmdBase>) - Method in Launcher

printConfig(CloudConfig, int) - Method in CmdCloud

Prints the cloud configuration in a human readable manner

println(DataflowReadChannel<?>, Closure) - Method in DataflowExtensions

Print the channel content to the console standard output

printMasterInstance(String, CloudConfig) - Method in CmdCloud

Prints the information about the cluster master instance

printOptions(Class) - Method in Launcher

printRecord(HashCode, TraceRecord) - Method in CmdLog

Print a log TraceRecord the the standard output by using the specified templateStr

printWorkerInstances(List<String>) - Method in CmdCloud

Prints the list of worker instances

privateFields() - Method in CascadingConfig

process(T) - Method in AbstractSplitter

Apply the splitting operation on the given object

process(Reader) - Method in AbstractTextSplitter

Process the object to split

process(String, Closure) - Method in BaseScript

Method to which is mapped the *process* declaration.

process(InputStream) - Method in BytesSplitter

process(Reader) - Method in CsvSplitter

Implements the CSV parsing

process(Reader) - Method in FastaSplitter

process(Reader) - Method in FastqSplitter

processChunk(def) - Method in AbstractTextSplitter

Add the fetched record to the current collection and emit a new chunk

ProcessConfig - Class in nextflow.processor

Holds the process configuration properties

ProcessConfig(ProcessConfig) - Constructor in ProcessConfig

processDeregister(TaskProcessor) - Method in Session

ProcessException - Class in nextflow.exception

Base class for process execution errors

ProcessFactory - Class in nextflow.processor

Factory class for {@TaskProcessor} instances

ProcessFactory(BaseScript, Session, Map) - Constructor in ProcessFactory

ProcessFailedException - Class in nextflow.exception

Thrown when a process script terminates by an error condition

processFile(Path, Path) - Method in PublishDir

processFileImpl(Path, Path) - Method in PublishDir

processItem(def) - Method in CollectFileOp

ProcessMissingTemplateException - Class in nextflow.exception

Exception raised the it is not possible to find the process template file

ProcessNotRecoverableException - Class in nextflow.exception

Exception thrown when a process contains an error not recoverable e.g. script compilation error, invalid resource request, etc.

processRegister(TaskProcessor) - Method in Session

ProcessStageException - Class in nextflow.exception

Exception thrown when an error is raised during the process file staging phase

ProcessSubmitException - Class in nextflow.exception

Exception thrown if the process submission returns an error

project - Field in RepositoryProvider

The pipeline qualified name following the syntax owner/repository

property(String, def) - Method in CustomPoolFactory

propertyMissing(String) - Method in CaptureProperties

propertyMissing(String) - Method in TraceRecord

ProviderConfig - Class in nextflow.scm

Models a repository provider configuration attributes

ProviderConfig(String) - Constructor in ProviderConfig

PublishDir - Class in nextflow.processor

Implements the publishDir directory.

PublishDir.Mode - Enum in nextflow.processor

publishOutputs(TaskRun) - Method in TaskProcessor

Publish output files to a specified target folder

put(String, Object) - Method in LazyMap

put(long, V) - Method in LevelDbSort

Put a value into the DB

put(Object, Object) - Method in ReadOnlyMap

Set a map entry only if it's not declared as read-only

put(String, Object) - Method in ScriptBinding.ParamsMap

A name-value pair to the map object.

put(String, Object) - Method in TaskConfig

put(String, Object) - Method in TaskContext

put(String, def) - Method in TraceRecord

putAll(Map) - Method in LazyMap

putAll(Map) - Method in ScriptBinding.ParamsMap

putAll(Map<String, Object>) - Method in TraceRecord

putIndexAsync(TaskHandler) - Method in CacheDB

putTaskAsync(TaskHandler) - Method in CacheDB

Q

qualityScore(Map) - Method in FastqSplitter

Retrieve the encoding quality score of the fastq file

queueInterval - Field in AbstractGridExecutor

queueStatusCommand(def) - Method in AbstractGridExecutor

@param queue The command for which the status of jobs has be to read

queueStatusCommand(def) - Method in CirrusExecutor

queueStatusCommand(Object) - Method in CondorExecutor

queueStatusCommand(Object) - Method in KubernetesExecutor

queueStatusCommand(def) - Method in LsfExecutor

queueStatusCommand(Object) - Method in NqsiiExecutor

queueStatusCommand(Object) - Method in PbsExecutor

queueStatusCommand(Object) - Method in SgeExecutor

queueStatusCommand(Object) - Method in SlurmExecutor

quote(Path) - Method in AbstractGridExecutor

quote - Field in CsvSplitter

The character used to wrap values containing a separator char

quote(Path) - Method in SgeExecutor

R

randomSample(DataflowReadChannel, int) - Method in DataflowExtensions

RandomSampleOp - Class in nextflow.extension

Implements Reservoir sampling of channel content

RandomSampleOp(DataflowReadChannel, int) - Constructor in RandomSampleOp

read(Kryo, Input) - Method in ArrayBag

read(Kryo, Input, Class<ArrayTuple>) - Method in ArrayTupleSerializer

read(Kryo, Input) - Method in BlankSeparatedList

read(Kryo, Input, Class<File>) - Method in FileSerializer

read(Kryo, Input, Class<GString>) - Method in GStringSerializer

read(Kryo, Input, Entry>) - Method in MapEntrySerializer

read(Kryo, Input, Class<Path>) - Method in PathSerializer

read(Kryo, Input, Class<Pattern>) - Method in PatternSerializer

read(Kryo, Input, Class<URL>) - Method in URLSerializer

read(Kryo, Input, Class<UUID>) - Method in UUIDSerializer

readBool() - Method in SequentialFileStore

readByte() - Method in SequentialFileStore

readBytes(String) - Method in BitbucketRepositoryProvider

readBytes(String) - Method in GithubRepositoryProvider

{@inheritDoc}

readBytes(String) - Method in GitlabRepositoryProvider

{@inheritDoc}

readBytes(String) - Method in LocalRepositoryProvider

readBytes(String) - Method in RepositoryProvider

Read the content of a file stored in the remote repository

readBytes(int) - Method in SequentialFileStore

readChar() - Method in SequentialFileStore

readExitStatus() - Method in GridTaskHandler

When a process terminated save its exit status into the file defined by #exitFile

readInt() - Method in SequentialFileStore

readLong() - Method in SequentialFileStore

readManifest() - Method in AssetManager

ReadOnlyMap - Class in nextflow.util

A class for which the initial values cannot be changed

ReadOnlyMap(Map, List<String>) - Constructor in ReadOnlyMap

@param map Initial map values

readShort() - Method in SequentialFileStore

readTemplate() - Method in TimelineObserver

readText(String) - Method in RepositoryProvider

recordFields - Field in AbstractSplitter

recordMode - Field in AbstractSplitter

recordToMap(String, String, String, String, Map) - Method in FastqSplitter

recordToText(String, String, String, String) - Method in FastqSplitter

reduce(DataflowReadChannel<?>, V, Closure<V>) - Method in DataflowExtensions

The reduce( ) operator applies a function of your choosing to the first item emitted by a source channel, then feeds the result of that function along with the second item emitted by the source channel into the same function, then feeds the result of that function along with the third item into the same function, and so on until all items have been emitted by the source channel.

reduceImpl(DataflowReadChannel<?>, DataflowVariable, def, Closure<V>) - Method in DataflowHelper

Implements the #reduce operator

register(def) - Method in Barrier

Register a "party" that is needed to wait the arrival

register() - Method in CirrusExecutor

register() - Method in Executor

Template method executed once for executor class

register(Class, def) - Method in KryoHelper

Register a new class - serializer pair

registerConditionalBlock(String, String) - Method in ComposedConfigSlurper

rehydrate(byte[], ClassLoader) - Method in TaskContext

Deserialize and create a new instance of the DelegateMap using the provided byte array serialized binary

RemoteSession - Class in nextflow.util

Make a script executable in a remote session, embedding the script classes and external libraries.

RemoteSession(Session) - Constructor in RemoteSession

Creates the object and compress the classes and libraries ina binary form

remove(TaskHandler) - Method in LocalPollingMonitor

When a task completes its execution remove it from tasks polling queue restoring the allocated resources i.e. cpus and memory

remove(TaskHandler) - Method in TaskPollingMonitor

Remove a task from task the scheduling queue

removeGlobStar(String) - Method in SimpleFileCopyStrategy

Remove a glob star specifier returning the longest parent path

removeTaskEntry(HashCode) - Method in CacheDB

render(String, Map) - Method in TaskTemplateEngine

render(TraceRecord) - Method in TraceFileObserver

Render a TraceRecord object to a string

render(List<String>, List<String>, String) - Method in TraceRecord

Render the specified list of fields to a single string value

renderCloudConfigObject() - Method in LaunchConfig

renderData() - Method in TimelineObserver

renderDocument(DAG, Path) - Method in CytoscapeHtmlRenderer

renderDocument(DAG, Path) - Method in CytoscapeJsRenderer

renderDocument(DAG, Path) - Method in DagRenderer

Render the dag to the specified file.

renderDocument(DAG, Path) - Method in DotRenderer

renderDocument(DAG, Path) - Method in GraphvizRenderer

Render the DAG using Graphviz to the specified file in a format specified in the constructor.

renderHtml() - Method in TimelineObserver

renderNetwork(DAG) - Method in CytoscapeJsRenderer

renderNetwork(DAG) - Method in DotRenderer

renderScript(def) - Method in TaskRun

renderTemplate(Path, boolean) - Method in TaskRun

Given a template script file and a binding, returns the rendered script content

RepositoryProvider - Class in nextflow.scm

Base class for a generic source repository provider

resolve(String, def) - Method in LazyMap

Resolve a directive *dynamic* value i.e. defined with a closure or lazy string

resolve(Map) - Method in ValueOutParam

Given the TaskContext object resolve the actual value to which this param is bound

resolveClassPaths(List<Path>) - Method in ConfigHelper

Given a list of paths looks for the files ending withe the extension '.jar' and return a list containing the original directories, plus the JARs paths

resolveDestination(def) - Method in PublishDir

resolveName(String) - Method in AssetManager

Given a project name or a repository URL returns a fully qualified project name.

resumeFromCache(CacheableCollector) - Method in AbstractSplitter

Emits the cache file chunks

resumeOrDie(TaskRun, Throwable) - Method in TaskProcessor

@param task The TaskRun instance that raised an error

ROLE_MASTER - Field in Const

ROLE_WORKER - Field in Const

root - Field in CmdPull

route(DataflowReadChannel, Closure) - Method in DataflowExtensions

run() - Method in CmdClean

Command entry method

run() - Method in CmdClone

run() - Method in CmdCloud

Command entry point

run() - Method in CmdConfig

run() - Method in CmdDrop

run() - Method in CmdFs

run() - Method in CmdHelp

run() - Method in CmdHistory

run() - Method in CmdInfo

run() - Method in CmdList

run() - Method in CmdLog

Implements the `log` command

run() - Method in CmdLs

run() - Method in CmdNode

run() - Method in CmdPull

run() - Method in CmdRun

run() - Method in CmdSelfUpdate

run() - Method in CmdView

run() - Method in Launcher

Launch the pipeline execution

run() - Method in ScriptRunner

Launch the Nextflow script execution

run() - Method in TaskProcessor

Launch the 'script' define by the code closure as a local bash script

runOptions - Field in ContainerBuilder

S

S3_UPLOADER_CLASS - Field in Const

S3FileCopyStrategy - Class in nextflow.executor

Defines the script operation to handle file when running in the Cirrus cluster

S3FileCopyStrategy(TaskBean) - Constructor in S3FileCopyStrategy

safeClose() - Method in FileCollector

A synchronised version of #close operation

safeProcessFile(Path, Path) - Method in PublishDir

saveFile(Closure<Path>) - Method in FileCollector

Save an collect entry to the respective grouping file

saveFile(Closure<Path>) - Method in SimpleFileCollector

{@inheritDoc}

saveFile(Closure<Path>) - Method in SortFileCollector

{@inheritDoc}

saveTo(Path) - Method in FileCollector

schedule(TaskHandler) - Method in TaskMonitor

Schedule a TaskHandler instance adding it to the queue of tasks to be processed.

schedule(TaskHandler) - Method in TaskPollingMonitor

Schedule a new task for execution

SCM_FILE - Field in ProviderConfig

ScriptBinding - Class in nextflow.script

Defines the script execution context.

ScriptBinding.ParamsMap - Class in nextflow.script

Holds parameter immutable values

ScriptBinding.ParamsMap(Map<String, Object>) - Constructor in ScriptBinding.ParamsMap

ScriptBinding(Map) - Constructor in ScriptBinding

Creates a new nextflow script binding object

ScriptFile - Class in nextflow.script

Runnable pipeline script file

ScriptFile(File) - Constructor in ScriptFile

ScriptFileCopyStrategy - Interface in nextflow.executor

Declares file operations used in the task wrapper script

ScriptRunner - Class in nextflow.script

Application main class

ScriptRunner.ArgsList - Class in nextflow.script

Extends an ArrayList class adding a nicer index-out-of-range error message

ScriptRunner.ArgsList(List<String>) - Constructor in ScriptRunner.ArgsList

ScriptRunner(Session) - Constructor in ScriptRunner

ScriptType - Enum in nextflow.script

The type of script declared by a process

sendPoisonPill() - Method in TaskProcessor

Send a poison pill over all the outputs channel

sep - Field in CsvSplitter

The CVS separator

separate(DataflowReadChannel, int, Closure) - Method in DataflowExtensions

SeparateOp - Class in nextflow.extension

Implements the DataflowExtensions.separate operator logic

SeparateOp(DataflowReadChannel, int, Closure<List<Object>>) - Constructor in SeparateOp

separatorChar - Field in FileOutParam

The character used to separate multiple names (pattern) in the output specification

SequentialFileStore - Class in nextflow.file

A buffered storage.

SequentialFileStore(Path, int) - Constructor in SequentialFileStore

serialize(def, File) - Method in KryoHelper

Serialize an object to the specified file

serialize() - Method in TaskContext

serialize() - Method in TraceRecord

ServiceName - Annotation Type in nextflow.util

Assign a name to a runtime loaded service object

Session - Class in nextflow

Holds the information on the current execution

Session(Map) - Constructor in Session

Create a new session given the configuration specified

session - Field in TaskProcessor

The current workflow execution session

set(DataflowReadChannel, Closure) - Method in DataflowExtensions

Assign the source channel to a global variable with the name specified by the closure.

setArgs(List<String>) - Method in ScriptBinding

The list of CLI arguments (unnamed)

setAttribute(K, V) - Method in CascadingConfig

setBackground(boolean) - Method in CmdNode

setBackground(boolean) - Method in CmdRun

setBaseDir(Path) - Method in ConfigBuilder

setBaseDir(Path) - Method in Session

setBinding(Map) - Method in ComposedConfigSlurper

Sets any additional variables that should be placed into the binding when evaluating Config scripts

setCached(boolean) - Method in TraceRecord

setClassLoader(ClassLoader) - Method in Session

setClusterName(String) - Method in CloudConfig

setCmdConfig(CmdConfig) - Method in ConfigBuilder

setCmdNode(CmdNode) - Method in ConfigBuilder

setCmdRun(CmdRun) - Method in ConfigBuilder

setConfigPath(Path) - Method in ComposedConfigScript

setConfigStack(Stack<Path>) - Method in ComposedConfigScript

setContext(Map) - Method in TaskConfig

Assign the context map for dynamic evaluation of task config properties

setCpus(String) - Method in ContainerBuilder

setCreateUser(boolean) - Method in CloudConfig

setCredentials(String, String) - Method in RepositoryProvider

setDaemon(boolean) - Method in LoggerHelper

setDelegate(Object) - Method in TaskClosure

setDriverName(String) - Method in CloudConfig

setEnableShortNotation(boolean) - Method in TaskTemplateEngine

setEnvironment(String) - Method in ComposedConfigSlurper

setFields(List<String>) - Method in TraceFileObserver

setFieldsAndFormats(def) - Method in TraceFileObserver

setForce(boolean) - Method in AssetManager

setIgnoreIncludes(boolean) - Method in ComposedConfigScript

setIgnoreIncludes(boolean) - Method in ComposedConfigSlurper

Disable parsing of includeConfig directive

setImageId(String) - Method in CloudConfig

SetInParam - Class in nextflow.script

setInput(InParam, Object) - Method in TaskRun

setInstanceType(String) - Method in CloudConfig

setKeyFile(Path) - Method in CloudConfig

setKeyHash(String) - Method in CloudConfig

setKeyName(String) - Method in CloudConfig

setLauncher(Launcher) - Method in CmdBase

setLibDir(String) - Method in Session

setLocalPath(File) - Method in AssetManager

setMapper(Closure) - Method in CrossOp

setMapper(Closure) - Method in PhaseOp

setMaxIndex(int) - Method in LoggerHelper

setMemory(def) - Method in ContainerBuilder

setMinIndex(int) - Method in LoggerHelper

setMode(PublishDir.Mode) - Method in PublishDir

setName(String) - Method in ContainerBuilder

setName(String) - Method in DockerBuilder

setOnComplete(Closure) - Method in DirWatcher

setOnComplete(Closure) - Method in WorkflowMetadata

Implements the following idiom in the pipeline script:

     workflow.onComplete = {
         // do something
     }
 

setOnError(Closure) - Method in WorkflowMetadata

Implements the following idiom in the pipeline script:

     workflow.onError = {
         // do something
     }
 

setOptions(CliOptions) - Method in ConfigBuilder

setOpts(Map) - Method in PhaseOp

SetOutParam - Class in nextflow.script

SetOutParam.CombineMode - Enum in nextflow.script

setOutput(OutParam, Object) - Method in TaskRun

setParams(Map) - Method in ComposedConfigSlurper

setParams(Map<String, Object>) - Method in ScriptBinding

The map of the CLI named parameters

setPassword(String) - Method in ProviderConfig

setPath(Path) - Method in PublishDir

setPivot(def) - Method in CombineOp

setPlaceholder(char) - Method in TaskTemplateEngine

setProfile(String) - Method in ConfigBuilder

setProperty(String, def) - Method in TaskContext

setRecordFields(Map) - Method in AbstractSplitter

setResolveStrategy(int) - Method in TaskClosure

setRole(String) - Method in CloudConfig

setRolling(boolean) - Method in LoggerHelper

setScript(String) - Method in ScriptRunner

setSingleton(boolean) - Method in OutputsList

setSort(def) - Method in SortFileCollector

setSpotPrice(String) - Method in CloudConfig

setStatus(TaskStatus) - Method in TaskHandler

Task status attribute setter.

setTemp(String) - Method in ContainerBuilder

setTempDir(Path) - Method in FileCollector

@param path the temporary directory to be used

setToken(String) - Method in ProviderConfig

setType(String) - Method in TaskBody

Given a code section literal sets the task body type and isShell flag

setup() - Method in LoggerHelper

setUser(String) - Method in ProviderConfig

setUserName(String) - Method in CloudConfig

setVariable(String, Object) - Method in ScriptBinding

SgeExecutor - Class in nextflow.executor

Execute a task script by running it on the SGE/OGE cluster

shebangLine(def) - Method in TaskProcessor

Returns:

A string 'she-bang' formatted to the added on top script to be executed.

ShifterBuilder - Class in nextflow.container

Wrap a task execution in a Shifter container

ShifterBuilder(String) - Constructor in ShifterBuilder

signal() - Method in TaskDispatcher

signal() - Method in TaskMonitor

Notify when a task terminates

signal() - Method in TaskPollingMonitor

Signal that a task has been completed

SimpleFileCollector - Class in nextflow.file

Helper class used to aggregate values having the same key to files

SimpleFileCollector() - Constructor in SimpleFileCollector

SimpleFileCopyStrategy - Class in nextflow.executor

Simple file strategy that stages input files creating symlinks and copies the output files using the cp command.

SimpleFileCopyStrategy(TaskBean) - Constructor in SimpleFileCopyStrategy

singleItemOrList(List<FileHolder>) - Method in TaskProcessor

singleton - Field in TaskProcessor

Whenever the process is executed only once

SingularityBuilder - Class in nextflow.container

Implements a builder for Singularity containerisation

SingularityBuilder(String) - Constructor in SingularityBuilder

size() - Method in Barrier

size() - Method in SequentialFileStore

size() - Method in SimpleFileCollector

@return The number of files in the appender accumulator

skipLines - Field in CsvSplitter

The number of lines to skip

SlurmExecutor - Class in nextflow.executor

Processor for SLURM resource manager (DRAFT)

SortFileCollector - Class in nextflow.file

Helper class used to aggregate values having the same key to files

SortFileCollector.IndexEntry - Class in nextflow.file

Hold a single entry in the tree-set

SortFileCollector.IndexEntry(Comparable, long, byte[]) - Constructor in SortFileCollector.IndexEntry

SortFileCollector.IndexSort - Class in nextflow.file

SortFileCollector.IndexSort(DB, Comparator) - Constructor in SortFileCollector.IndexSort

sourceFile - Field in AbstractSplitter

SPLASH - Field in Const

split() - Method in AbstractSplitter

Start the slitting

split() - Method in SplitterStrategy

splitOverChannel(DataflowReadChannel, SplitterStrategy, Map) - Method in SplitterFactory

Implements dynamic method extension for splitter operators

SplitterFactory - Class in nextflow.splitter

Factory class for splitter objects

SplitterStrategy - Interface in nextflow.splitter

Interface that splitters object must implements

spread(DataflowReadChannel, Object) - Method in DataflowExtensions

stageInCommand(String, String, String) - Method in SimpleFileCopyStrategy

stageInputFile(Path, String) - Method in CirrusFileCopyStrategy

{@inheritDoc}

stageInputFile(Path, String) - Method in S3FileCopyStrategy

{@inheritDoc}

stageInputFile(Path, String) - Method in SimpleFileCopyStrategy

Stage the input file into the task working area.

stageOutCommand(String, String, String) - Method in SimpleFileCopyStrategy

Compose a `cp` or `mv` command given the source and target paths

start() - Method in Session

start() - Method in TaskDispatcher

Flag the dispatcher as started

start() - Method in TaskMonitor

Start the monitoring activity for the queued tasks

start() - Method in TaskPollingMonitor

Launch the monitoring thread

state - Field in TaskProcessor

The state is maintained by using an agent

status(boolean) - Method in CmdInfo

StdInParam - Class in nextflow.script

Represents a process *stdin* input parameter

StdOutParam - Class in nextflow.script

Model the process *stdout* parameter

STOP - Field in Channel

stop() - Method in Nextflow

Interrupts the iteration when using a split operators

StopSplitIterationException - Class in nextflow.exception

Stop the split iteration.

StopSplitIterationException() - Constructor in StopSplitIterationException

StringSplitter - Class in nextflow.splitter

Simple slitter chunking a string in sub-strings having the specified length

stripBlanks - Field in CsvSplitter

When true remove leading and trailing blanks from a value

submit() - Method in CachedTaskHandler

submit() - Method in GridTaskHandler

submit(TaskHandler) - Method in LocalPollingMonitor

Submits a task for execution allocating the resources (cpus and memory) requested by the task

submit() - Method in LocalTaskHandler

submit() - Method in NativeTaskHandler

submit() - Method in NopeTaskHandler

submit(TaskRun, boolean) - Method in TaskDispatcher

Submit the specified task for execution to the underlying system and add it to the queue of tasks to be monitored.

submit() - Method in TaskHandler

Submit the task for execution.

submit(TaskHandler) - Method in TaskPollingMonitor

Submits the specified task for execution adding it to the queue of scheduled tasks

submitLoop() - Method in TaskPollingMonitor

Wait for new tasks and submit for execution when a slot is available

submitPendingTasks() - Method in TaskPollingMonitor

Loop over the queue of pending tasks and submit all of which satisfy the canSubmit(nextflow.processor.TaskHandler) condition

submitTask(TaskRun, HashCode, Path) - Method in TaskProcessor

Execute the specified task shell script

subscribe(DataflowReadChannel<V>, Map<String, Closure>) - Method in DataflowExtensions

Subscribe *onNext*, *onError* and *onComplete*

subscribeImpl(DataflowReadChannel<V>, Map<String, Closure>) - Method in DataflowHelper

Subscribe *onNext*, *onError* and *onComplete*

sum(DataflowQueue, Closure) - Method in DataflowExtensions

The sum operators crates a channel that emits the sum of all values emitted by the source channel to which is applied

SupportedScriptTypes - Annotation Type in nextflow.executor

Define the script type runnable by the executor

systemOsName - Field in BashWrapperBuilder

T

TAG_CLUSTER_NAME - Field in CloudConst

TAG_CLUSTER_ROLE - Field in CloudConst

tagInstances(Collection<String>, Map<String, String>) - Method in AmazonCloudDriver

tagInstances(Collection<String>, LaunchConfig) - Method in CloudDriver

Tags the specified instances with the default tags

take(DataflowReadChannel<V>, int) - Method in DataflowExtensions

emit only the first n items emitted by an Observable

tap(DataflowReadChannel, DataflowWriteChannel) - Method in DataflowExtensions

TapOp - Class in nextflow.extension

Implements the DataflowExtensions.tap operator

TapOp(DataflowReadChannel, DataflowWriteChannel) - Constructor in TapOp

Create the operator instance

target(def) - Method in AbstractSplitter

Set the target object to be splitter.

target - Field in LazyMap

The target map holding the values

target(def) - Method in SplitterStrategy

Abstract splitter method

target - Field in ValueOutParam

TASK_CONTEXT_PROPERTY_NAME - Field in TaskProcessor

TaskBean - Class in nextflow.processor

Serializable task value object.

TaskBean(TaskRun) - Constructor in TaskBean

TaskBody - Class in nextflow.script

Holds process script meta-data

TaskBody(Closure, String, String, TokenValRef) - Constructor in TaskBody

taskBody - Field in TaskProcessor

The piece of code to be execute provided by the user

TaskClosure - Class in nextflow.script

Extends a groovy.lang.Closure class adding the source attribute

TaskClosure(Closure, String) - Constructor in TaskClosure

TaskConfig - Class in nextflow.processor

Task local configuration properties

TaskConfig(Map<String, Object>) - Constructor in TaskConfig

TaskContext - Class in nextflow.processor

Map used to delegate variable resolution to script scope

TaskContext() - Constructor in TaskContext

ONLY FOR TEST PURPOSE -- do not use

TaskDispatcher - Class in nextflow.processor

Monitor tasks execution for completion notifying their results

TaskDispatcher() - Constructor in TaskDispatcher

TaskEntry - Class in nextflow.processor

@author Paolo Di Tommaso

TaskFault - Class in nextflow.processor

Model a task execution fault

TaskHandler - Class in nextflow.processor

Actions to handle the underlying job running the user task.

TaskHandler() - Constructor in TaskHandler

Only for testing purpose

TaskId - Class in nextflow.processor

TaskRun unique identifier

TaskId() - Constructor in TaskId

Default constructor is only required to enable class serialisation by Kryo library.

TaskMonitor - Interface in nextflow.processor

Declares the methods for scheduling and handling tasks

TaskPollingMonitor - Class in nextflow.processor

Monitors the queued tasks waiting for their termination

TaskPollingMonitor(Map) - Constructor in TaskPollingMonitor

Create the task polling monitor with the provided named parameters object.

TaskProcessor - Class in nextflow.processor

@author Paolo Di Tommaso

TaskProcessor.BaseProcessInterceptor - Class in nextflow.processor

TaskProcessor.BaseProcessInterceptor(List<DataflowChannel>, boolean) - Constructor in TaskProcessor.BaseProcessInterceptor

TaskProcessor.RunType - Enum in nextflow.processor

TaskProcessor.RunType(String) - Constructor in TaskProcessor.RunType

TaskProcessor.TaskProcessorInterceptor - Class in nextflow.processor

Intercept dataflow process events

TaskProcessor.TaskProcessorInterceptor(List<DataflowChannel>, boolean) - Constructor in TaskProcessor.TaskProcessorInterceptor

TaskProcessor(String, Executor, Session, BaseScript, ProcessConfig, TaskBody) - Constructor in TaskProcessor

Create and initialize the processor object

TaskRun - Class in nextflow.processor

Models a task instance

TaskStatus - Enum in nextflow.processor

Defines possible task statuses

TaskTemplateEngine - Class in nextflow.processor

A template engine that uses ch.grengine.Grengine to parse template scripts It also that ignore dollar variable and uses a custom character for variable interpolation

TaskTemplateEngine(Grengine) - Constructor in TaskTemplateEngine

temp - Field in ContainerBuilder

tempDir(String, boolean) - Method in Nextflow

@return Create a temporary directory

tempFile(String, boolean) - Method in Nextflow

@return Create a temporary file

template(def) - Method in TaskContext

Helper method to be used inside a process to load a script template.

terminate() - Method in DirWatcher

terminate() - Method in ScriptRunner

terminateInstances(Collection<String>) - Method in AmazonCloudDriver

terminateInstances(Collection<String>) - Method in CloudDriver

Terminate one or more cloud instances

terminateProcess() - Method in TaskProcessor

test(String, List<String>) - Method in ScriptRunner

Test the name specified by the methodName

TextFileCollector - Class in nextflow.splitter

A collector strategy that creates a chunks as text files

TextFileCollector(Path, Charset) - Constructor in TextFileCollector

TextSplitter - Class in nextflow.splitter

Split a text file by one or more lines at times

TimelineObserver - Class in nextflow.trace

Render pipeline timeline processes execution

TimelineObserver(Path) - Constructor in TimelineObserver

toCloudConfigObject() - Method in LaunchConfig

toConfigObject0(Map) - Method in CascadingConfig

toConfigObject() - Method in CascadingConfig

Convert this object to an equivalent groovy.util.ConfigObject

toConfigObject() - Method in LaunchConfig

toDouble(DataflowReadChannel) - Method in DataflowExtensions

toFloat(DataflowReadChannel) - Method in DataflowExtensions

toInteger(DataflowReadChannel) - Method in DataflowExtensions

TokenEnvCall - Class in nextflow.script

Token used by the DSL to identify a environment variable declaration, like this

     input:
     set( env(X), ... )
     

TokenFileCall - Class in nextflow.script

A token used by the DSL to identify a 'file' declaration in a 'set' parameter, for example:

      input:
      set( file('name'), ... )
      

TokenFileCall(def) - Constructor in TokenFileCall

TokenStdinCall - Class in nextflow.script

An object of this class replace the stdin token in input map declaration.

TokenStdoutCall - Class in nextflow.script

An object of this class replace the stdout token in input map declaration.

TokenValCall - Class in nextflow.script

This class is used to identify a 'val' when used like in this example:

  input:
  set ( val(x), ...  )

TokenValRef - Class in nextflow.script

TokenValRef(String, int, int) - Constructor in TokenValRef

TokenVar - Class in nextflow.script

Presents a variable definition in the script context.

toList(DataflowReadChannel<V>) - Method in DataflowExtensions

Convert a DataflowQueue alias *channel* to a Java List

toList() - Method in HistoryFile.Record

ToListOp - Class in nextflow.extension

Implements DataflowExtensions.toList operator

ToListOp(DataflowReadChannel) - Constructor in ToListOp

toLong(DataflowReadChannel) - Method in DataflowExtensions

toSortedList(DataflowReadChannel<V>, Closure) - Method in DataflowExtensions

Convert a DataflowQueue alias *channel* to a Java List sorting its content

toString() - Method in AssetManager.RevisionInfo

@return A formatted string containing the commitId and revision properties

toString() - Method in BaseParam

toString() - Method in BatchCleanup

@return A string listing the IDs of the jobs to be killed

toString() - Method in BlankSeparatedList

toString() - Method in CharSequenceCollector

toString() - Method in CloudConfig

toString() - Method in CloudInstanceType

toString() - Method in HexIdentity

toString() - Method in HistoryFile.Record

toString() - Method in LazyMap

toString() - Method in ProviderConfig

toString() - Method in TaskBody

toString() - Method in TaskContext

toString() - Method in TaskHandler

toString() - Method in TaskId

toString() - Method in TaskRun

toString() - Method in TraceRecord

toString() - Method in WorkflowMetadata

@return Render the workflow properties

toStringBuilder(StringBuilder) - Method in GridTaskHandler

toStringBuilder(StringBuilder) - Method in TaskHandler

touchFile(Path) - Method in CirrusFileCopyStrategy

{@inheritDoc}

touchFile(Path) - Method in S3FileCopyStrategy

{@inheritDoc}

touchFile(Path) - Method in ScriptFileCopyStrategy

Command to 'touch' a file

touchFile(Path) - Method in SimpleFileCopyStrategy

{@inheritDoc}

TraceFileObserver - Class in nextflow.trace

Create a CSV file containing the processes execution information

TraceFileObserver() - Constructor in TraceFileObserver

ONLY FOR TESTING PURPOSE

TraceObserver - Interface in nextflow.trace

Defines the defaults method for application flow observer

TraceRecord - Class in nextflow.trace

This object represent holds the information of a single process run, its content is saved to a trace file line

TraceRecord() - Constructor in TraceRecord

Trie - Class in nextflow.util

Implements a basic Trie data structure

Trie(T) - Constructor in Trie

TRUNCATE - Field in FileCollector

tryFallbackWithSplitter(def, String, Object, Exception) - Method in SplitterFactory

This method try to invoke a splitter or a counter method dynamically

tryReadFromStdin() - Method in CmdRun

tuple(Object) - Method in Nextflow

Creates a nextflow.util.ArrayTuple object with the given open array items

type - Field in FileOutParam

The type of path to output, either file, dir or any

U

UdockerBuilder - Class in nextflow.container

Wrap a task execution in a Udocker container

UdockerBuilder(String) - Constructor in UdockerBuilder

unique(DataflowReadChannel<V>, Closure) - Method in DataflowExtensions

A convenience method for making a collection unique using a Closure to determine duplicate (equal) items.

until(DataflowReadChannel<T>, Closure<Boolean>) - Method in DataflowExtensions

unzip(byte[], Path) - Method in RemoteSession

Unzip a byte array buffer into a target java.io.File folder

update(Agent, Closure) - Method in DataflowExtensions

INTERNAL ONLY API

update(String, boolean, Date) - Method in HistoryFile

updateModules() - Method in AssetManager

URLSerializer - Class in nextflow.util

usage(List<String>) - Method in CmdCloud

Print the command usage help

usage(List<String>) - Method in CmdCloud.CreateCluster

usage(List<String>) - Method in CmdCloud.JoinCluster

usage(List<String>) - Method in CmdCloud.ListNodes

usage(List<String>) - Method in CmdCloud.Shutdown

usage(List<String>) - Method in CmdCloud.SpotPrices

usage(List<String>) - Method in CmdCloud.SubCmd

usage(List<String>) - Method in CmdFs

Print the command usage help

usage() - Method in CmdFs.SubCmd

usage(String) - Method in Launcher

Print the usage string for the given command - or - the main program usage string if not command is specified

usage(List<String>) - Method in UsageAware

UsageAware - Interface in nextflow.cli

Command can implement this interface to provide a custom usage description

useRawNumbers(boolean) - Method in TraceFileObserver

UUIDSerializer - Class in nextflow.util

V

validate(LaunchConfig) - Method in AmazonCloudDriver

validate(CloudDriver) - Method in CloudConfig

validate(LaunchConfig) - Method in CloudDriver

Validate the cloud configuration object

validateConfigFiles(List<String>) - Method in ConfigBuilder

Transform the specified list of string to a list of files, verifying their existence.

validateFor(String) - Method in RepositoryProvider

Validate the repository for the specified file.

validateInputSets(List) - Method in TaskProcessor

validFields() - Method in CascadingConfig

validOptions() - Method in AbstractSplitter

Returns:

A map representing the valid options for the splitter.

validOptions() - Method in AbstractTextSplitter

Returns:

A map representing the valid options for the splitter.

validOptions() - Method in CsvSplitter

Returns:

A map representing the valid options for the splitter.

validOptions() - Method in FastaSplitter

validOptions() - Method in FastqSplitter

validOptions() - Method in StringSplitter

Returns:

A map representing the valid options for the splitter.

value(def) - Method in Channel

value() - Method in ConfigField

@default ''

Returns:

The field name (default: empty string)

value() - Method in ServiceName

value() - Method in SupportedScriptTypes

ValueInParam - Class in nextflow.script

Represents a process *value* input parameter

ValueOutParam - Class in nextflow.script

Model a process *value* output parameter

variable(T) - Method in Nextflow

Create a DataflowVariable binding it to the specified value

varToConst(Expression) - Method in NextflowDSLImpl

varToStr(Expression) - Method in NextflowDSLImpl

verifyAndTrackHistory(String, String) - Method in ScriptRunner

@param cli The launcher command line string

view(DataflowReadChannel<?>, Closure) - Method in DataflowExtensions

visit(ASTNode, SourceUnit) - Method in NextflowDSLImpl

visitClosureExpression(ClosureExpression) - Method in NextflowDSLImpl.GStringToLazyVisitor

visitDeclarationExpression(DeclarationExpression) - Method in NextflowDSLImpl.VariableVisitor

visitGStringExpression(GStringExpression) - Method in NextflowDSLImpl.GStringToLazyVisitor

visitPropertyExpression(PropertyExpression) - Method in NextflowDSLImpl.VariableVisitor

visitVariableExpression(VariableExpression) - Method in NextflowDSLImpl.VariableVisitor

VOID - Field in Channel

W

waitInstanceStatus(Collection<String>, CloudInstanceStatus) - Method in AmazonCloudDriver

waitInstanceStatus(Collection<String>, CloudInstanceStatus) - Method in CloudDriver

Wait the list of specified instance to be in `running` state

watchPath(Path, String) - Method in Channel

WORKDIR - Field in TraceRecord

WorkflowMetadata - Class in nextflow.script

Models workflow metadata properties and notification handler

WorkflowMetadata(ScriptRunner) - Constructor in WorkflowMetadata

Initialise the available workflow properties

wrapExpressionWithClosure(BlockStatement, Expression, int, CharSequence, SourceUnit) - Method in NextflowDSLImpl

Wrap a generic expression with in a closure expression

wrapHeader(String) - Method in AbstractGridExecutor

wrapHeader(String) - Method in LsfExecutor

wrapReader(Reader) - Method in AbstractTextSplitter

Wrap the target object with a java.io.BufferedReader filter stream

wrapWithClosure(Expression) - Method in NextflowDSLImpl.GStringToLazyVisitor

write(Kryo, Output) - Method in ArrayBag

write(Kryo, Output, ArrayTuple) - Method in ArrayTupleSerializer

write(Kryo, Output) - Method in BlankSeparatedList

write(Kryo, Output, File) - Method in FileSerializer

write(Kryo, Output, GString) - Method in GStringSerializer

write(String, UUID, String, def, Date) - Method in HistoryFile

write(Kryo, Output, Entry) - Method in MapEntrySerializer

write(Kryo, Output, Path) - Method in PathSerializer

write(Kryo, Output, Pattern) - Method in PatternSerializer

write(Kryo, Output, URL) - Method in URLSerializer

write(Kryo, Output, UUID) - Method in UUIDSerializer

writeBool(boolean) - Method in SequentialFileStore

writeByte(byte) - Method in SequentialFileStore

writeBytes(byte[]) - Method in SequentialFileStore

writeChar(char) - Method in SequentialFileStore

writeInt(int) - Method in SequentialFileStore

writeLong(long) - Method in SequentialFileStore

writeShort(short) - Method in SequentialFileStore

X

xformToLazy(GStringExpression) - Method in NextflowDSLImpl.GStringToLazyVisitor

Y

Z

zip(Path) - Method in RemoteSession

Zip the folder content recursively and return a byte[] object

_

_file(String) - Method in SimpleFileCollector

_in_each(def) - Method in ProcessConfig

_in_env(def) - Method in ProcessConfig

_in_file(def) - Method in ProcessConfig

_in_set(Object) - Method in ProcessConfig

_in_stdin(def) - Method in ProcessConfig

_in_val(def) - Method in ProcessConfig

_out_file(Object) - Method in ProcessConfig

_out_set(Object) - Method in ProcessConfig

_out_stdout(def) - Method in ProcessConfig

_out_val(Object) - Method in ProcessConfig

_private() - Method in ConfigField

Mark the configuration field as private