.toList() to .fromList()

[RamilNurtdinov]

Bug report

Expected behavior and actual behavior

Greetings from CRG.
I want to run some channel and store the report in a (list) value
I want to use this list many times.
From my point of view .toList() to .fromList() should be compatible.

Steps to reproduce the problem

current_list = Channel.from(1, 2, 3, 4).toList()
current_list.view()
executions = Channel.fromList( current_list )
executions.view()

Program output

Cannot invoke method view() on null object

Environment

• Nextflow version: N E X T F L O W ~ version 22.10.1
• Java version: openjdk 17.0.3-internal 2022-04-19
• Operating system: Linux
• Bash version: GNU bash, version 4.2.46(1)-release (x86_64-redhat-linux-gnu)
  CRG cluster

Additional context

[jemunro]

You can use the operator flatMap to perform the opposite action to toList

current_list = Channel.from(1, 2, 3, 4).toList()
current_list.view()
executions = current_list.flatMap()
executions.view()

[RamilNurtdinov]

Hi Jacob

This is exact solution I needed, thank you.
I read my TSV index file and combine all lines inside with toList().
flatMap extracts necessary fields and makes new channel.

[mribeirodantas]

Hello, @RamilNurtdinov. You're under the misconception that .toList() returns a [regular Groovy] list, when actually it returns a Nextflow channel that consists of a sole element which is a list. The fromList channel factory expects a regular Groovy list, and that's why fromList and toList don't go hand-in-hand.

In DSL1, you could obtain the regular Groovy list from a channel outputted by toList through the .value property, but this does not work in DSL2 anymore, as it's anti-pattern. When writing your Nextflow pipeline, you should use the Nextflow Domain-Specific Language and, for Nextflow, information is always contained within a channel 😄

If you want to use a channel multiple times, this should be a value channel and that's exactly what the toList and collect operators do. If you want to iterate through the elements of this list within a channel, for example, you can use subscribe, map, among other operators.

[RamilNurtdinov]

Thank you Marcel

I got practical answer above that works in DSL2.