Index (nf-commons 20.04.1 API)

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

add(int, E) - Method in ArrayTuple
add(LabelDecorator) - Method in TextLabel
addAll(int, Collection<? extends E>) - Method in ArrayTuple
after(String, def, Closure) - Method in Throttle: Allows at most one execution after the specified time delay returning initialValue before the first execution, and the cached result value the following times
ALPHA - Field in FileHelper
append(List) - Method in TableBuilder: Append the specified list of values as the next row in the table, the columns width are adapted accordingly
apply(TextLabel, String) - Method in LabelDecorator
applyMax(String) - Method in TextLabel
ArrayTuple - Class in nextflow.util: Provides a basic tuple implementation extending an java.util.ArrayList and not allowing any content change operation
ArrayTuple(int) - Constructor in ArrayTuple
asBoolean() - Method in Duration
asBoolean() - Method in MemoryUnit
asList(String, String) - Method in CmdLineHelper
asPath(URI) - Method in FileHelper: Given a java.net.URI return a java.nio.file.Path object eventually creating the associated file system if required
asType(File, Class<Object>) - Method in Bolts: Converts a File to a Path object
await(long) - Method in ByteDumper: Await that the thread finished to read the process stdout

B

Bag - Interface in nextflow.util: Marker interface that define that the collection does not care about items order
bestMatches(Collection<String>, String) - Method in Bolts: Find all the best matches for the given example string in a list of values
between(Temporal, Temporal) - Method in Duration
Bolts - Class in nextflow.extension: Generic extensions
ByteBufferBackedInputStream - Class in nextflow.io: An InputStream adaptor which reads data from a ByteBuffer
ByteBufferBackedInputStream(ByteBuffer) - Constructor in ByteBufferBackedInputStream
ByteDumper - Class in nextflow.io: @author Paolo Di Tommaso
ByteDumper(File, Closure) - Constructor in ByteDumper

C

cache(Object, long, Closure<V>) - Method in Throttle
CacheFunnel - Interface in nextflow.util: Interface to delegate cache hashing to a the implementing object
CacheHelper - Class in nextflow.util: Provide helper method to handle caching
CacheHelper.HashMode - Enum in nextflow.util
canExecute(Path) - Method in FilesEx: Tests whether the application can execute the file denoted by this abstract pathname.
canRead(Path) - Method in FilesEx: Tests whether the application can read the file denoted by this abstract pathname.
canWrite(Path) - Method in FilesEx: Tests whether the application can modify the file denoted by this abstract pathname.
capitalize(String) - Method in Bolts
CharsetHelper - Class in nextflow.util: @author Paolo Di Tommaso
CheckHelper - Class in nextflow.util: Validation helper
checkIfExists(Path, Map) - Method in FileHelper
checkParams(String, Map<String, ?>, String) - Method in CheckHelper: Verify that all method named parameters are included in the provided list
cleanUp() - Method in Global
clear() - Method in ArrayTuple
cli(String) - Method in Escape
cloneAsLazy(GString, def) - Method in Bolts: Create a copy of a groovy.lang.GString object cloning all values that are instance of groovy.lang.Closure
cloneWith(T, def) - Method in Bolts: Clone a groovy.lang.Closure object and set the specified map as delegate object in the resulting closure
close() - Method in LogOutputStream: Writes all remaining data from the buffer.
close() - Method in ReaderInputStream: Close the stream.
close() - Method in SkipLinesInputStream
close() - Method in WriterOutputStream: Close the stream.
closeQuietly(Closeable) - Method in FilesEx: Close a file in safe manner i.e. without throwing eventual exception raised by the *close* operation
closeRow() - Method in TableBuilder: Close a row in the @return
closest(Collection<String>, String) - Method in Bolts: Find all the best matches for the given example string in a list of values
CmdLineHelper - Class in nextflow.util: @author Paolo Di Tommaso
CmdLineHelper(String) - Constructor in CmdLineHelper
CollectionHelper - Class in nextflow.util: @author Paolo Di Tommaso
compareTo(Duration, Object) - Method in Duration
compareTo(MemoryUnit, Object) - Method in MemoryUnit
compareTo(Object) - Method in VersionNumber: Implements version number comparator logic
complete(Path) - Method in FilesEx: A shortcut for java.nio.file.Path#toAbsolutePath() and java.nio.file.Path#normalize()
consume() - Method in ByteDumper
consumeHeader() - Method in SkipLinesInputStream
contains(String) - Method in CmdLineHelper
copyPath(Path, Path, CopyOption) - Method in FileHelper: Move a path to a target destination.
copyTo(Path, String) - Method in FilesEx: Copy or a file or a directory content.
createDirIfNotExists(File) - Method in FilesEx
createLocalDir(String) - Method in FileHelper
createTempFolder(Path) - Method in FileHelper
CsvParser - Class in nextflow.util: Simple comma-separated-values parser

D

DataInputStreamAdapter - Class in nextflow.io: Implements a java.io.InputStream object backed on a java.io.DataInput instance
DataInputStreamAdapter(DataInput) - Constructor in DataInputStreamAdapter
DataOutputStreamAdapter - Class in nextflow.io: Implements a java.io.OutputStream object backed on a java.io.DataOutput instance
DataOutputStreamAdapter(DataOutput) - Constructor in DataOutputStreamAdapter
DATETIME_FORMAT - Field in Bolts
debug1(Logger, Map, Object) - Method in Bolts: Append a `debug` level entry in the application log.
defaultHasher() - Method in CacheHelper
delete(Path) - Method in FilesEx: Deletes the file or directory denoted by this abstract pathname.
deleteDir(Path) - Method in FilesEx: Deletes a directory with all contained files and subdirectories.
deleteOnExit(Path) - Method in FilesEx
deletePath(Path) - Method in FileHelper: Delete a path or a directory.
deserialize(byte[], ClassLoader) - Method in InputStreamDeserializer: Deserialize an object given its bytes representation and a custom class-loader
div(Number) - Method in Duration
div(Path, Path) - Method in FilesEx
div(Number) - Method in MemoryUnit
Duration - Class in nextflow.util: A simple time duration representation
Duration(long, TimeUnit) - Constructor in Duration

E

empty(Path) - Method in FileHelper
empty(Path) - Method in FilesEx: Check if a file - or - a directory is empty
envFor(String) - Method in FileHelper: Lazy create and memoize this object since it will never change
equals(Object) - Method in VersionNumber
error1(Logger, Map, Object) - Method in Bolts: Append a `error` level entry in the application log.
Escape - Class in nextflow.util: Escape helper class
escape(String) - Method in FilePatternSplitter: Escape pattern meta-characters with a backslash
every(String, Closure) - Method in Throttle: Executes the specified code block and returns the resulting value.
exists(Path, LinkOption) - Method in FilesEx

F

FileHelper - Class in nextflow.file: Provides some helper method handling files
FileHolder - Class in nextflow.file: Implements a special Path used to stage files in the work area
FileHolder(def, Path, def) - Constructor in FileHolder
FileMutex - Class in nextflow.file: Implements a mutual exclusive file lock strategy to prevent two or more JVMs/process to access the same file or resource
FileMutex(File) - Constructor in FileMutex
FilePatternSplitter - Class in nextflow.file: Parse a file path to isolate the parent, file-name and whenever it contains a glob|regex pattern
FilePatternSplitter.Syntax - Enum in nextflow.file
FilePatternSplitter(FilePatternSplitter.Syntax) - Constructor in FilePatternSplitter
FilesEx - Class in nextflow.extension: Add utility methods to standard classes File and Path
fileSystemForScheme(String) - Method in FileHelper
FileSystemPathFactory - Class in nextflow.file: Generic interface
firstMetaIndex(String) - Method in FilePatternSplitter
flatten(Collection, Closure) - Method in CollectionHelper
flush() - Method in LogOutputStream: Flush this log stream.
flush() - Method in WriterOutputStream: Flush the stream.
fmtDate(Date, TimeZone) - Method in SysHelper: Given a java.util.Date object convert to a string representation according the DATE_FORMAT
format(Date, String, TimeZone) - Method in Bolts: Format a java.util.Date object
format(String) - Method in Duration: Duration formatting utilities and constants.
funnel(Hasher, HashMode) - Method in CacheFunnel

G

getArg(String) - Method in CmdLineHelper

getAt(int) - Method in VersionNumber

Retrieve the i-th component in a version number

getAvailCpus() - Method in SysHelper

@return The number of CPUs available

getAvailDisk() - Method in SysHelper

@return The actual free space in the node local storage

getAvailMemory() - Method in SysHelper

@return The total system memory available

getAwsClientConfig() - Method in Global

getAwsCredentials() - Method in Global

getAwsProfile0(Map) - Method in Global

getAwsRegion(Map, Map) - Method in Global

getBaseDir() - Method in ISession

The folder where the main script is contained

getBaseName(Path, int) - Method in FilesEx

Gets the base name, minus the full path and extension, from a full filename.

getBinding() - Method in ISession

@return The global script binding object

getBool(String, String, boolean) - Method in IniFile

getBootTimeMillis() - Method in SysHelper

getBootTimeString() - Method in SysHelper

getBytes() - Method in MemoryUnit

getCharset(def) - Method in CharsetHelper

getConfig() - Method in ISession

Holds the configuration object

getDays() - Method in Duration

getDefaultPathMatcher(String) - Method in FileHelper

Returns a PathMatcher that performs match operations on the String representation of java.nio.file.Path objects by interpreting a given pattern.

getDouble(String, String, double) - Method in IniFile

getErrMessage(Throwable) - Method in Bolts

getExtension(Path) - Method in FilesEx

Retrieve the file name extension

getFile() - Method in IniFile

getFileName() - Method in FilePatternSplitter

getFileName() - Method in StagePath

getFloat(String, String, float) - Method in IniFile

getGiga() - Method in MemoryUnit

getHeader() - Method in SkipLinesInputStream

getHostName() - Method in SysHelper

@return The system host name

getHours() - Method in Duration

getIdentifier(Path, String) - Method in FileHelper

@return

Parameters:: script

getInt(String, String, int) - Method in IniFile

getKilo() - Method in MemoryUnit

getLibDir() - Method in ISession

@return List of path added to application classpath at runtime

getLocalCachePath(Path, Path, UUID) - Method in FileHelper

Given a path look for an existing file with that name in the cacheDir folder.

getLocalTempPath() - Method in FileHelper

getMajor() - Method in VersionNumber

@return The major version number ie. the first component

getMega() - Method in MemoryUnit

getMessageLevel() - Method in LogOutputStream

@return the trace level of the log system

getMillis() - Method in Duration

getMinor() - Method in VersionNumber

@return The minor version number ie. the second component

getMinutes() - Method in Duration

getName(Path) - Method in FilesEx

Extend Path adding a getName method semantically equivalent to File#getName

getOrCreate(Map<K, V>, K, V) - Method in Bolts

getOrCreateFileSystemFor(String, Map) - Method in FileHelper

getOrInstallProvider(Class<T>) - Method in FileHelper

Get the instance of the specified FileSystemProvider class.

getParent() - Method in FilePatternSplitter

getPatch() - Method in VersionNumber

@return The minor version number ie. the third component

getPathFsType(Path) - Method in FileHelper

getPathMatcherFor(String, FileSystem) - Method in FileHelper

Get a path matcher for the specified file system and file pattern.

getPermissions(Path) - Method in FilesEx

Get the file Unix permission as a string e.g.

getProperty(String) - Method in StagePath

getProviderFor(String) - Method in FileHelper

Returns a java.nio.file.spi.FileSystemProvider for a file scheme

getRate() - Method in RateUnit

@return The actual rate unit as a double

getRateLimiter() - Method in RateUnit

Create a com.google.common.util.concurrent.RateLimiter object for rate unit

getScheme() - Method in FilePatternSplitter

getScheme(Path) - Method in FilesEx

getScriptName() - Method in ISession

The pipeline script name (without parent path)

getSeconds() - Method in Duration

getSession() - Method in Global

@return The object instance representing the current session

getSimpleName(Path) - Method in FilesEx

Extend Path adding a getSimpleName() method which returns the file base name removing all file extension.

getStageName() - Method in FileHolder

getStorePath() - Method in FileHolder

getString(String, String, String) - Method in IniFile

getUniqueId() - Method in ISession

The unique identifier of this session

getUptimeDuration() - Method in SysHelper

The system uptime

getUptimeText() - Method in SysHelper

Read the system uptime as returned by the uptime Linux tool

getUri(File) - Method in FilesEx

getUrlProtocol(String) - Method in FileHelper

getWorkDir() - Method in ISession

The folder where tasks temporary files are stored

getWorkDirFileSystem() - Method in FileHelper

NOTE: this cannot be accessed by a remote system

getWorkDirIsNFS() - Method in FileHelper

@return true when the current session working directory is a NFS mounted path false otherwise

getWorkFolder(Path, HashCode) - Method in FileHelper

Defines a cacheable path for the specified HashCode instance.

GLOB_CURLY_BRACKETS - Field in FilePatternSplitter

GLOB - Field in FilePatternSplitter

GLOB_SQUARE_BRACKETS - Field in FilePatternSplitter

Global - Class in nextflow

Hold global variables

Globs - Class in nextflow.file

Helper class to access sun.nio.fs.Globs#toRegexPattern(java.lang.String, boolean) method

H

hasExited() - Method in PosixProcess: Check if the submitted job has terminated its execution
hashCode() - Method in VersionNumber
hasher(Hasher, Object, CacheHelper.HashMode) - Method in CacheHelper
hasNext() - Method in QuoteStringTokenizer
head(Path, int, def) - Method in FilesEx: Read the top from the beginning of a Path object, stopping as soon as 'n' lines has been read.
head(String, Align) - Method in TableBuilder

I

indent(String, String) - Method in Bolts: Indent each line in the given test by a specified prefix
info1(Logger, Map, Object) - Method in Bolts: Append a `info` level entry in the application log.
IniFile - Class in nextflow.util: Read a INI file
IniFile(String) - Constructor in IniFile
InputStreamDeserializer - Class in nextflow.util: A object deserializer that allows you to specify a custom class loader
InputStreamDeserializer(InputStream, ClassLoader) - Constructor in InputStreamDeserializer
invokeMethod(String, Object) - Method in StagePath
isAllLowerCase(String) - Method in Bolts: Check if ALL characters in a string are lowercase.
isAllUpperCase(String) - Method in Bolts: Check if ALL characters in a string are uppercase.
isCacheable() - Method in ISession
isCamelCase(String) - Method in Bolts
isDirectory(Path, LinkOption) - Method in FilesEx
ISession - Interface in nextflow: Nextflow session interface
isFile(Path, LinkOption) - Method in FilesEx
isGlobAllowed(Path) - Method in FileHelper
isHidden(Path) - Method in FilesEx
isLink(Path) - Method in FilesEx
isLowerCase(String) - Method in Bolts: Check if a alphabetic characters in a string are lowercase.
isMatchingPattern(def) - Method in FilePatternSplitter
isPathNFS(Path) - Method in FileHelper: Check if the specified path is a NFS mount
isPattern() - Method in FilePatternSplitter
isResumeMode() - Method in ISession
isUpperCase(String) - Method in Bolts: Check if a alphabetic characters in a string are uppercase.
isValid(def, def) - Method in CheckHelper: Check if the provide value is included in the specified range
iterator() - Method in ArrayTuple
iterator() - Method in QuoteStringTokenizer

J

K

L

LabelDecorator - Interface in nextflow.ui

A generic decorator for TextLabel class

lastModified(Path, LinkOption) - Method in FilesEx

Returns the time that the file denoted by this abstract pathname was last modified.

left() - Method in TextLabel

leftShift(def) - Method in TableBuilder

Defines the left-shift operator useful to build the table using the following syntax

      def table = new TableBuilder()
      table << col1 << col2 << col3 << table.closeRow()
      :

leftShift(LabelDecorator) - Method in TextLabel

leftTrim(String) - Method in Bolts

Remove blank chars at string beginning

list(Path) - Method in FilesEx

List the content of a given path folder.

listDirectory(Path) - Method in FileHelper

List the content of a file system path

listFiles(Path, Closure<Boolean>) - Method in FilesEx

List the content of a given path folder.

listIterator(int) - Method in ArrayTuple

load(Reader) - Method in IniFile

load() - Method in ServiceDiscover

lock(Closure<T>) - Method in FileMutex

LogOutputStream - Class in nextflow.io

Base class to connect a logging system to the output and/or error stream of then external process.

LogOutputStream(int) - Constructor in LogOutputStream

Creates a new instance of this class.

M

matches(File, String) - Method in FilesEx
matches(String) - Method in VersionNumber: Checks if the version number satisfies the specified condition.
max(int) - Method in TextLabel
MemoryUnit - Class in nextflow.util: Represent a memory unit
MemoryUnit(String) - Constructor in MemoryUnit: Create a memory unit instance with the given semantic string
minus(Duration) - Method in Duration
minus(Path, int) - Method in FilesEx
minus(MemoryUnit) - Method in MemoryUnit
mkdir(Path, FileAttribute<?>) - Method in FilesEx: Creates the directory named by this abstract pathname
mkdirs(Path, FileAttribute<?>) - Method in FilesEx: Creates the directory named by this abstract pathname, including any necessary but nonexistent parent directories
mklink(Path, Map) - Method in FilesEx
movePath(Path, Path, CopyOption) - Method in FileHelper: Move a path to a target destination.
moveTo(Path, String) - Method in FilesEx
multiply(Number) - Method in Duration
multiply(Number) - Method in MemoryUnit

N

nameParts(String) - Method in FileHelper
names() - Method in ServiceDiscover
navigate(Map, String, def) - Method in Bolts
next() - Method in QuoteStringTokenizer
normalizeAwsClientConfig(Map<String, ?>) - Method in Global: Convert configuration keys from camel-case notation (nextflow) to underscore separated notation expected by the AWS client
normalizeDuration(Map<String, ?>, String) - Method in Global
normalizeMemUnit(Map<String, ?>, String) - Method in Global
normalizePath(String) - Method in FileHelper
number() - Method in TextLabel

O

of(Object) - Method in CacheHelper.HashMode: Provide helper method to handle caching
of(String, Duration) - Method in Duration
of(long) - Method in MemoryUnit
of(String) - Method in RateUnit
of(def) - Method in TextLabel: Create a new TextLabel object with the specified value
onShutdown(Closure) - Method in Global: Run the specified closure on application termination
or(Path, Path) - Method in FilesEx

P

pairs(Map, Map) - Method in Bolts
parse(String) - Method in CsvParser
parse(String) - Method in FilePatternSplitter: Parse a file path detecting the schema, parent folder, file name and pattern components
parse(String) - Method in FileSystemPathFactory
parse(String) - Method in RateUnit
parseNext(String) - Method in QuoteStringTokenizer
parseQuote(String, char) - Method in QuoteStringTokenizer
parseUri(String) - Method in FileSystemPathFactory
path(GString) - Method in Escape
plus(Duration) - Method in Duration
plus(Path, Path) - Method in FilesEx
plus(MemoryUnit) - Method in MemoryUnit
PosixProcess - Class in nextflow.util: Hack the Java process to be able to access the Unix process id
PosixProcess(Process) - Constructor in PosixProcess
processBuffer() - Method in LogOutputStream: Converts the buffer to a string and sends it to processLine.
processLine(String, int) - Method in LogOutputStream: Logs a line to the log system of the user.
propertyMissing(String) - Method in IniFile

Q

QUESTION_MARK_REGEX - Field in FilePatternSplitter
QuoteStringTokenizer - Class in nextflow.util: Split a string into literal tokens i.e. sequence of chars that does not contain a blank or wrapper by a quote or double quote
QuoteStringTokenizer(String, char) - Constructor in QuoteStringTokenizer

R

randomString(int) - Method in FileHelper
RateUnit - Class in nextflow.util: Model am execution rate limit measure unit
RateUnit(String) - Constructor in RateUnit: Create a rate unit using a string annotation as `10 sec` ie. 10 per second or `100 / 5 min` 100 events each 5 minutes
read(byte[], int, int) - Method in ByteBufferBackedInputStream
read() - Method in DataInputStreamAdapter
read() - Method in ReaderInputStream: Read a single byte.
read() - Method in SkipLinesInputStream
readAttributes(Path, LinkOption) - Method in FileHelper
readAttributes(Path) - Method in FilesEx
ReaderInputStream - Class in nextflow.io: java.io.InputStream implementation that reads a character stream from a java.io.Reader and transforms it to a byte stream using a specified charset encoding.
ReaderInputStream(Reader) - Constructor in ReaderInputStream: Construct a new ReaderInputStream that uses the default character encoding with a default input buffer size of 1024 characters.
regex() - Method in FilePatternSplitter
relativize0(Path, Path) - Method in FileHelper
remove(int) - Method in ArrayTuple
remove() - Method in QuoteStringTokenizer
removeAll(Collection<?>) - Method in ArrayTuple
renameTo(Path, String) - Method in FilesEx
replaceMetaChars(String, char) - Method in FilePatternSplitter
resolveClass(ObjectStreamClass) - Method in InputStreamDeserializer
resolveSymLink(File) - Method in FilesEx
retainAll(Collection<?>) - Method in ArrayTuple
right() - Method in TextLabel
rightTrim(String) - Method in Bolts: Remove blank chars at the end of the string
rollFile(Path, int) - Method in FilesEx: Roll a file moving to a new path whose name ends with .1
run() - Method in ByteDumper

S

section(String) - Method in IniFile
ServiceDiscover - Class in nextflow.util: A service loader inspired to java.util.ServiceLoader that allows to load only service names or classes without instantiating the actual instances
ServiceDiscover(Class<S>, ClassLoader) - Constructor in ServiceDiscover
set(int, E) - Method in ArrayTuple
setErrorMessage(String) - Method in FileMutex
setExecutable(Path, boolean, boolean) - Method in FilesEx: Sets the owner's or everybody's execute permission for the specified file.
setHeaders(TextLabel) - Method in TableBuilder
setLastModified(Path, long) - Method in FilesEx: Sets the last-modified time of the file or directory named by this Path.
setMaxColsWidth(int) - Method in TableBuilder
setPermissions(File, int, int, int) - Method in FilesEx: Set the file Unix permission using the digit representing the respectively the permissions for the owner, the group and others.
setProperty(String, Object) - Method in StagePath
setQuote(String) - Method in CsvParser
setReadable(Path, boolean, boolean) - Method in FilesEx: A convenience method to set the owner's read permission for the specified file
setReadOnly(Path) - Method in FilesEx: Marks the file or directory named by this abstract pathname so that only read operations are allowed.
setSeparator(String) - Method in CsvParser
setSession(ISession) - Method in Global: Set the application session object
setStrip(boolean) - Method in CsvParser
setTimeout(def) - Method in FileMutex
setWaitMessage(String) - Method in FileMutex
setWritable(Path, boolean, boolean) - Method in FilesEx: Sets the owner's or everybody's write permission for the specified file.
size() - Method in VersionNumber: @return The number of components in the version number eg new VersionNumber('2.3.12').size() == 3
skip(long) - Method in DataInputStreamAdapter
skip(long) - Method in SkipLinesInputStream
SkipLinesInputStream - Class in nextflow.io: An input stream that skips the first `n` lines in a text stream
SkipLinesInputStream(InputStream, int) - Constructor in SkipLinesInputStream: Creates a FilterInputStream by assigning the argument in to the field this.in so as to remember it for later use.
splitter(String) - Method in CmdLineHelper: Given a string the splitter method separate it by blank returning a list of string.
StagePath - Class in nextflow.file: @author Paolo Di Tommaso
StagePath(String) - Constructor in StagePath
STAR_CHAR_REGEX - Field in FilePatternSplitter
strip(String, String) - Method in Bolts
strip(String) - Method in FilePatternSplitter: Strips backslash characters from a path
stripEnd(String, String) - Method in Bolts
stripStart(String, String) - Method in Bolts
subList(int, int) - Method in ArrayTuple
switchOff() - Method in TextLabel: Switch OFF the decorators rendering
switchOn() - Method in TextLabel: Turn ON the decorators rendering
SysHelper - Class in nextflow.util: System helper methods

T

TableBuilder - Class in nextflow.ui: Used to render text based table for UI purpose.
tail(File, int, def, int) - Method in FilesEx: Read the last 'n' lines from a File without reading all the file content
terminate() - Method in ByteDumper: Interrupt the dumper thread
TextLabel - Class in nextflow.ui: @author Paolo Di Tommaso
TextLabel.Align - Enum in nextflow.ui
TextLabel(def) - Constructor in TextLabel: Create a label with the provided value
Throttle - Class in nextflow.util: Limit the execution of a code block on a specified time basis
Throttle.ThrottleObj - Class in nextflow.util
Throttle.ThrottleObj(def, long) - Constructor in Throttle.ThrottleObj
toBytes() - Method in MemoryUnit
toConfigObject(Map) - Method in Bolts
toDays() - Method in Duration
toDuration(Number) - Method in Bolts
toGiga() - Method in MemoryUnit
toHours() - Method in Duration
toKilo() - Method in MemoryUnit
toLine(List<String>) - Method in CmdLineHelper
toMap(ConfigObject) - Method in Bolts: Converts ConfigObjects to a plain Map
toMega() - Method in MemoryUnit
toMemory(Number) - Method in Bolts
toMillis() - Method in Duration
toMinutes() - Method in Duration
toRealPath(LinkOption) - Method in StagePath
toSeconds() - Method in Duration
toString() - Method in Duration
toString() - Method in MemoryUnit
toString() - Method in QuoteStringTokenizer
toString() - Method in RateUnit
toString() - Method in StagePath
toString() - Method in TableBuilder: @return Render the final table and return the string
toString() - Method in TextLabel: @return Renders the string applying the provided decorators
toString() - Method in VersionNumber
toUnit(String) - Method in MemoryUnit: Function to parse/convert given memory unit
toUnixRegexPattern(String) - Method in Globs
toUriString(Path) - Method in FilesEx
trace1(Logger, Map, Object) - Method in Bolts: Append a `trace` level entry in the application log.
trace(Logger, Object, Throwable) - Method in Bolts
trackWidths(List<Integer>) - Method in TableBuilder
trimDotZero(String) - Method in Bolts: Remove the left side after a dot (including it) e.g.
tryLock(Lock, Closure) - Method in Bolts: Invokes the specify closure only if it is able to acquire a lock

U

uncapitalize(String) - Method in Bolts
UNITS - Field in Duration
UNITS - Field in MemoryUnit
uriPath(Path) - Method in Escape
URL_PROTOCOL - Field in FileHelper

V

VersionNumber - Class in nextflow.util: Model a semantic version number
VersionNumber(String) - Constructor in VersionNumber: Create a version number object
visitFiles(Map, Path, String, Closure) - Method in FileHelper: Applies the specified action on one or more files and directories matching the specified glob pattern

W

warn1(Logger, Map, Object) - Method in Bolts: Append a `warn` level entry in the application log.
width(int) - Method in TextLabel
wildcards(String) - Method in Escape
withLock(Path, Duration, Closure) - Method in Bolts: Creates a file system wide lock that prevent two or more JVM instances/process to work on the same file
withName(def) - Method in FileHolder
write(int) - Method in DataOutputStreamAdapter
write(byte[], int, int) - Method in LogOutputStream: Write a block of characters to the output stream
write(int) - Method in WriterOutputStream: Write a single byte to the stream.
WriterOutputStream - Class in nextflow.io: java.io.OutputStream implementation that transforms a byte stream to a character stream using a specified charset encoding and writes the resulting stream to a java.io.Writer.
WriterOutputStream(Writer) - Constructor in WriterOutputStream: Constructs a new WriterOutputStream that uses the default character encoding and with a default output buffer size of 1024 characters.