Channels

In Nextflow, channels are the key data structures that facilitate the dataflow dependencies between each step (i.e. process) in a pipeline.

There are two kinds of channels, queue channels and value channels. Channels are created using channel factories and transformed using channel operators.

Queue channels

A queue channel is a channel that emits an asynchronous sequence of values.

A queue channel can be created by channel factories (e.g., channel.of and channel.fromPath), operators (e.g., map and filter), and processes (see Process outputs).

The values in a queue channel cannot be accessed directly – they can only be accessed by passing the channel as input to an operator or process. For example:

channel.of(1, 2, 3).view { v -> "queue channel emits ${v}" }

queue channel emits 1
queue channel emits 2
queue channel emits 3

Value channels

A value channel is a channel that is bound to an asynchronous value.

A value channel can be created with the channel.value factory, certain operators (e.g., collect and reduce), and processes (under certain conditions).

The value in a value channel cannot be accessed directly – it can only be accessed by passing the channel as input to an operator or process. For example:

channel.value(1).view { v -> "value channel is ${v}" }

value channel is 1

Channel factories

Channel factories are functions that create channels from regular values.

The channel.fromPath() factory creates a channel from a file name or glob pattern, similar to the files() function:

channel.fromPath('input/*.txt').view()

See Channel factories for the full list of channel factories.

Operators

Channel operators, or operators for short, are functions that consume and produce channels. Because channels are asynchronous, operators are necessary to manipulate the values in a channel. Operators are particularly useful for implementing glue logic between processes.

Commonly used operators include:

combine: emit the combinations of two channels
collect: collect the values from a channel into a list
filter: select the values in a channel that satisfy a condition
flatMap: transform each value from a channel into a list and emit each list element separately
groupTuple: group the values from a channel based on a grouping key
join: join the values from two channels based on a matching key
map: transform each value from a channel with a mapping function
mix: emit the values from multiple channels
view: print each value in a channel to standard output

See Operators for the full list of operators.