Channels

Nextflow is based on the Dataflow programming model in which processes communicate through channels.

A channel is a non-blocking unidirectional FIFO queue which connects two processes. It has two properties:

  1. Sending a message is an asynchronous operation which completes immediately, without having to wait for the receiving process.
  2. Receiving data is a blocking operation which stops the receiving process until the message has arrived.

Channel factory

Channels may be created implicitly by the process output(s) declaration or explicitly using the following channel factory methods.

The available factory methods are:

create

Creates a new channel by using the create method, as shown below:

channelObj = Channel.create()

from

The from method allows you to create a channel emitting any sequence of values that are specified as the method argument, for example:

ch = Channel.from( 1, 3, 5, 7 )
ch.subscribe { println "value: $it" }

The first line in this example creates a variable ch which holds a channel object. This channel emits the values specified as a parameter in the from method. Thus the second line will print the following:

value: 1
value: 3
value: 5
value: 7

The following example shows how to create a channel from a range of numbers or strings:

zeroToNine = Channel.from( 0..9 )
strings = Channel.from( 'A'..'Z' )

Note

Note that when the from argument is an object implementing the (Java) Collection interface, the resulting channel emits the collection entries as individual emissions.

Thus the following two declarations produce an identical result even tough in the first case the items are specified as multiple arguments while in the second case as a single list object argument:

Channel.from( 1, 3, 5, 7, 9 )
Channel.from( [1, 3, 5, 7, 9] )

But when more than one argument is provided, they are always managed as single emissions. Thus, the following example creates a channel emitting three entries each of which is a list containing two elements:

Channel.from( [1, 2], [5,6], [7,9] )

value

This method creates a dataflow variable that is a channel to which one entry, at most, can be bound. An optional not null value can be specified as a parameters, which is bound to the newly created channel. For example:

expl1 = Channel.value()
expl2 = Channel.value( 'Hello there' )
expl3 = Channel.value( [1,2,3,4,5] )

The first line in the example creates an 'empty' variable. The second line creates a channel and binds a string to it. Finally the last one creates a channel and binds a list object to it that will be emitted as a sole emission.

fromPath

You can create a channel emitting one or more file paths by using the fromPath method and specifying a path string as an argument. For example:

myFileChannel = Channel.fromPath( '/data/some/bigfile.txt' )

The above line creates a channel and binds to it a Path item referring the specified file.

Note

It does not check the file existence.

Whenever the fromPath argument contains a * or ? wildcard character it is interpreted as a glob path matcher. For example:

myFileChannel = Channel.fromPath( '/data/big/*.txt' )

This example creates a channel and emits as many Path items as there are files with txt extension in the /data/big folder.

Tip

Two asterisks, i.e. **, works like * but crosses directory boundaries. This syntax is generally used for matching complete paths. Curly brackets specify a collection of sub-patterns.

For example:

files = Channel.fromPath( 'data/**.fa' )
moreFiles = Channel.fromPath( 'data/**/*.fa' )
pairFiles = Channel.fromPath( 'data/file_{1,2}.fq' )

The first line returns a channel emitting the files ending with the suffix .fa in the data folder and recursively in all its sub-folders. While the second one only emits the files which have the same suffix in any sub-folder in the data path. Finally the last example emits two files: data/file_1.fq and data/file_2.fq.

Note

As in Linux BASH the * wildcard does not match against hidden files (i.e. files whose name start with a . character).

In order to include hidden files, you need to start your pattern with a period character or specify the hidden: true option. For example:

expl1 = Channel.fromPath( '/path/.*' )
expl2 = Channel.fromPath( '/path/.*.fa' )
expl3 = Channel.fromPath( '/path/*', hidden: true )

The first example returns all hidden files in the specified path. The second one returns all hidden files ending with the .fa suffix. Finally the last example returns all files (hidden and non-hidden) in that path.

By default a glob pattern only looks for regular file paths that match the specified criteria, i.e. it won't return directory paths.

You may use the parameter type specifying the value file, dir or any in order to define what kind of paths you want. For example:

myFileChannel = Channel.fromPath( '/path/*b', type: 'dir' )
myFileChannel = Channel.fromPath( '/path/a*', type: 'any' )

The first example will return all directory paths ending with the b suffix, while the second will return any file and directory starting with a a prefix.

Name Description
glob When true interprets characters *, ?, [] and {} as glob wildcards, otherwise handles them as normal characters (default: true)
type Type of paths returned, either file, dir or any (default: file)
hidden When true includes hidden files in the resulting paths (default: false)
maxDepth Maximum number of directory levels to visit (default: no limit)
followLinks When true it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: true)
relative When true returned paths are relative to the top-most common directory (default: false)

fromFilePairs

The fromFilePairs method creates a channel emitting the file pairs matching a glob pattern provided by the user. The matching files are emitted as tuples in which the first element is the grouping key of the matching pair and the second element is the list of files (sorted in lexicographical order). For example:

Channel
    .fromFilePairs('/my/data/SRR*_{1,2}.fastq')
    .println()

It will produce an output similar to the following:

[SRR493366, [/my/data/SRR493366_1.fastq, /my/data/SRR493366_2.fastq]]
[SRR493367, [/my/data/SRR493367_1.fastq, /my/data/SRR493367_2.fastq]]
[SRR493368, [/my/data/SRR493368_1.fastq, /my/data/SRR493368_2.fastq]]
[SRR493369, [/my/data/SRR493369_1.fastq, /my/data/SRR493369_2.fastq]]
[SRR493370, [/my/data/SRR493370_1.fastq, /my/data/SRR493370_2.fastq]]
[SRR493371, [/my/data/SRR493371_1.fastq, /my/data/SRR493371_2.fastq]]

Note

The glob pattern must contain at least a star wildcard character.

Alternatively it is possible to implement a custom file pair grouping strategy providing a closure which, given the current file as parameter, returns the grouping key. For example:

Channel
    .fromFilePairs('/some/data/*', size: -1) { file -> file.extension }
    .println { ext, files -> "Files with the extension $ext are $files" }

Table of optional parameters available:

Name Description
type Type of paths returned, either file, dir or any (default: file)
hidden When true includes hidden files in the resulting paths (default: false)
maxDepth Maximum number of directory levels to visit (default: no limit)
followLinks When true it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: true)
size Defines the number of files each emitted item is expected to hold (default: 2). Set to -1 for any.
flat When true the matching files are produced as sole elements in the emitted tuples (default: false).

watchPath

The watchPath method watches a folder for one or more files matching a specified pattern. As soon as there is a file that meets the specified condition, it is emitted over the channel that is returned by the watchPath method. The condition on files to watch can be specified by using * or ? wildcard characters i.e. by specifying a glob path matching criteria.

For example:

Channel
   .watchPath( '/path/*.fa' )
   .subscribe { println "Fasta file: $it" }

By default it watches only for new files created in the specified folder. Optionally, it is possible to provide a second argument that specifies what event(s) to watch. The supported events are:

Name Description
create A new file is created (default)
modify A file is modified
delete A file is deleted

You can specified more than one of these events by using a comma separated string as shown below:

Channel
   .watchPath( '/path/*.fa', 'create,modify' )
   .subscribe { println "File created or modified: $it" }

Warning

The watchPath factory waits endlessly for files that match the specified pattern and event(s). Thus, whenever you use it in your script, the resulting pipeline will never finish.

See also: fromPath factory method.

empty

The empty factory method, by definition, creates a channel that doesn't emit any value.

See also: ifEmpty and close operators.

Binding values

Since in Nextflow channels are implemented using dataflow variables or queues. Thus sending a message is equivalent to bind a value to object representing the communication channel.

bind( )

Channel objects provide a bind( ) method which is the basic operation to send a message over the channel. For example:

myChannel = Channel.create()
myChannel.bind( 'Hello world' )

operator <<

The operator << is just a syntax sugar for the bind( ) method. Thus, the following example produce an identical result as the previous one:

myChannel = Channel.create()
myChannel << 'Hello world'

Observing events

subscribe( )

The subscribe( ) method permits to execute a user define function each time a new value is emitted by the source channel.

The emitted value is passed implicitly to the specified function. For example:

// define a channel emitting three values
source = Channel.from ( 'alpha', 'beta', 'delta' )

// subscribe a function to the channel printing the emitted values
source.subscribe {  println "Got: $it"  }
Got: alpha
Got: beta
Got: delta

Note

Formally the user defined function is a Closure as defined by the Groovy programming language on which the Nextflow scripts are based on.

If needed the closure parameter can be defined explicitly, using a name other than it and, optionally, specifying the expected value type, as showed in the following example:

Channel
    .from( 'alpha', 'beta', 'lambda' )
    .subscribe { String str ->
        println "Got: ${str}; len: ${str.size()}"
     }
Got: alpha; len: 5
Got: beta; len: 4
Got: lambda; len: 6

Read Closures paragraph to learn more about closure feature.

onNext, onComplete, and onError

The subscribe() method may accept one or more of the following event handlers:

  • onNext: registers a function that is invoked whenever the channel emits a value. This is the same as using the subscribe( ) with a plain closure as describe in the examples above.
  • onComplete: registers a function that is invoked after the last value is emitted by the channel.
  • onError: registers a function that it is invoked when an exception is raised while handling the onNext event. It will not make further calls to onNext or onComplete. The onError method takes as its parameter the Throwable that caused the error.

For example:

Channel
    .from( 1, 2, 3 )
    .subscribe onNext: { println it }, onComplete: { println 'Done.' }
1
2
3
Done.