Channel factories
empty
The channel.empty
factory method, by definition, creates a channel that doesn’t emit any value.
See also: ifEmpty.
from
Deprecated since version 19.09.0-edge: Use channel.of or channel.fromList instead.
The channel.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
When the channel.from
argument is an object implementing the (Java) Collection interface, the resulting channel emits the collection entries as individual items.
Thus the following two declarations produce an identical result even though 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] )
fromList
New in version 19.10.0.
The channel.fromList
method allows you to create a channel emitting the values provided as a list of elements, for example:
channel
.fromList( ['a', 'b', 'c', 'd'] )
.view { "value: $it" }
Prints:
value: a
value: b
value: c
value: d
See also: channel.of factory method.
fromPath
You can create a channel emitting one or more file paths by using the channel.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 it to a Path object for the specified file.
Note
channel.fromPath
does not check whether the file exists.
Whenever the channel.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 catch hidden files (i.e. files whose name starts with a .
character).
Multiple paths or glob patterns can be specified using a list:
channel.fromPath( ['/some/path/*.fq', '/other/path/*.fastq'] )
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 can use the type
option 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 or directory starting with a a
prefix.
Available options:
checkIfExists
When
true
throws an exception of the specified path do not exist in the file system (default:false
)followLinks
When
true
it follows symbolic links during directories tree traversal, otherwise they are managed as files (default:true
)glob
When
true
interprets characters*
,?
,[]
and{}
as glob wildcards, otherwise handles them as normal characters (default:true
)hidden
When
true
includes hidden files in the resulting paths (default:false
)maxDepth
Maximum number of directory levels to visit (default: no limit)
relative
When
true
returned paths are relative to the top-most common directory (default:false
)type
Type of paths returned, either
file
,dir
orany
(default:file
)
fromFilePairs
The channel.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')
.view()
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 one *
wildcard character.
Multiple glob patterns can be specified using a list:
channel.fromFilePairs( ['/some/data/SRR*_{1,2}.fastq', '/other/data/QFF*_{1,2}.fastq'] )
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 }
.view { ext, files -> "Files with the extension $ext are $files" }
Available options:
checkIfExists
When
true
throws an exception of the specified path do not exist in the file system (default:false
)followLinks
When
true
it follows symbolic links during directories tree traversal, otherwise they are managed as files (default:true
)flat
When
true
the matching files are produced as sole elements in the emitted tuples (default:false
).hidden
When
true
includes hidden files in the resulting paths (default:false
)maxDepth
Maximum number of directory levels to visit (default: no limit)
size
Defines the number of files each emitted item is expected to hold (default: 2). Set to
-1
for any.type
Type of paths returned, either
file
,dir
orany
(default:file
)
fromSRA
New in version 19.04.0.
The channel.fromSRA
method queries the NCBI SRA database and returns a channel emitting the FASTQ files matching the specified criteria i.e project or accession number(s). For example:
channel
.fromSRA('SRP043510')
.view()
It returns:
[SRR1448794, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/004/SRR1448794/SRR1448794.fastq.gz]
[SRR1448795, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/005/SRR1448795/SRR1448795.fastq.gz]
[SRR1448792, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/002/SRR1448792/SRR1448792.fastq.gz]
[SRR1448793, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/003/SRR1448793/SRR1448793.fastq.gz]
[SRR1910483, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/003/SRR1910483/SRR1910483.fastq.gz]
[SRR1910482, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/002/SRR1910482/SRR1910482.fastq.gz]
(remaining omitted)
Multiple accession IDs can be specified using a list object:
ids = ['ERR908507', 'ERR908506', 'ERR908505']
channel
.fromSRA(ids)
.view()
[ERR908507, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_2.fastq.gz]]
[ERR908506, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_2.fastq.gz]]
[ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]]
Note
Each read pair is implicitly managed and returned as a list of files.
This method uses the NCBI ESearch API behind the scenes, therefore it allows the use of any query term supported by this API.
To access the ESearch API, you must provide your NCBI API keys through one of the following ways:
The
apiKey
option:channel.fromSRA(ids, apiKey:'0123456789abcdef')
The
NCBI_API_KEY
variable in your environment:export NCBI_API_KEY=0123456789abcdef
Available options:
apiKey
NCBI user API key.
cache
Enable/disable the caching API requests (default:
true
).max
Maximum number of entries that can be retried (default: unlimited) .
protocol
Allow choosing the protocol for the resulting remote URLs. Available choices:
ftp
,http
,https
(default:ftp
).
interval
The interval
method emits an incrementing index (starting from zero) at a periodic interval. For example:
Channel.interval('1s').view()
The above snippet will emit 0, 1, 2, and so on, every second, forever. You can use an operator such as take or until to close the channel based on a stopping condition.
An optional closure can be used to transform the index. Additionally, returning Channel.STOP
will close the channel. For example:
ch = Channel.interval('1s') { i ->
i == 10 ? Channel.STOP : i
}
ch.view()
of
New in version 19.10.0.
The channel.of
method allows you to create a channel that emits the arguments provided to it, for example:
ch = channel.of( 1, 3, 5, 7 )
ch.view { "value: $it" }
The first line in this example creates a variable ch
which holds a channel object. This channel emits the arguments
supplied to the of
method. Thus the second line prints the following:
value: 1
value: 3
value: 5
value: 7
Ranges of values are expanded accordingly:
channel
.of(1..23, 'X', 'Y')
.view()
Prints:
1
2
3
4
:
23
X
Y
See also: channel.fromList factory method.
topic
New in version 23.11.0-edge.
Note
This feature requires the nextflow.preview.topic
feature flag to be enabled.
A topic channel is a queue channel that can receive values from many source channels implicitly based on a matching topic name.
Tip
You can think of it as a channel that is shared across many different processes using the same topic name.
A process output can be assigned to a topic using the topic
option on an output, for example:
process foo {
output:
val('foo'), topic: my_topic
}
process bar {
output:
val('bar'), topic: my_topic
}
The channel.topic
method allows referencing the topic channel with the specified name, which can be used as a process
input or operator composition as any other Nextflow channel:
channel.topic('my-topic').view()
This approach is a convenient way to collect related items from many different sources without explicitly connecting them (e.g. using the mix
operator).
Warning
Any process that consumes a topic channel (directly or indirectly) should not send any outputs to that topic, or else the pipeline will hang forever.
See also: Generic options for process outputs.
value
The channel.value
method is used to create a value channel. An optional (not null
) argument can be specified to bind
the channel to a specific value. 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. The third line creates a channel and binds a list object to it that will be emitted as a single value.
watchPath
The channel.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:
create
: A new file is created (default)modify
: A file is modifieddelete
: A file is deleted
You can specify 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 channel.watchPath
factory waits endlessly for files that match the specified pattern and event(s), which means
that it will cause your pipeline to run forever. Consider using the take
or until
operator to close the channel when
a certain condition is met (e.g. after receiving 10 files, receiving a file named DONE
).
See also: channel.fromPath factory method.