Channels and Operators

Channels are asynchronous, which means that outputs from a set of processes will not necessarily be produced in the same order as the corresponding inputs went in. However, the first element into a channel queue is the first out of the queue (First in - First out). This allows processes to run as soon as they receive input from a channel. Channels only send data in one direction, from a producer (a process/operator), to a consumer (another process/operator).

Channels types

Nextflow distinguishes between two different kinds of channels: queue and value channels.

1. Queue channel

Queue channels are a type of channel in which data is consumed (used up) to make input for a process/operator. Queue channels can be created in two ways:

• As the outputs of a process.
• Explicitly using channel factory methods such as Channel.of or Channel.fromPath.

2. Value channels

The second type of Nextflow channel is a value channel. A value channel is bound to a single value (singleton). A value channel can be used an unlimited number times since its content is not consumed. This is also useful for processes that need to reuse input from a channel, for example, a reference genome sequence file that is required by multiple steps within a process, or by more than one process.

In Nextflow DSL1 queue channels can only be used once in a workflow, either connecting workflow input to process input, or process output to input for another process. In DSL2 we can use a queue channel multiple times.

Queue channel factory

Queue (consumable) channels can be created using the following channel factory methods.

• Channel.of
• Channel.fromList
• Channel.fromPath
• Channel.fromFilePairs
• Channel.fromSRA

ch1 = Channel.value('GRCh38')

ch2 = Channel.value(['chr1','chr2','chr3','chr4','chr5'])

chromosome_ch = Channel.of( 'chr1','chr3','chr5','chr7')

ch1.mix(ch2).collect()

Channel.fromPath(“/data/yeast/reads/*”)

Channel.fromPath(“/data/yeast/reads/*_{1,2}.fq”)

Channel.fromFilePairs(“/data/yeast/reads/*_{1,2}.fq”,size:2)

Filtering

filter(Number)

Transforming

map({it.replaceAll(“chr”,””)})

flatten()

collect()

collect()

Milestones

Nextflow milestones

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