Use channels in .groovy file or include classes defined in another .nf module

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1

I’m trying to create a groovy class that manipulates channels.

I can do this if I define the class within the .nf file that uses it. But if I try to move the class to a separate .nf file, or put it in a .groovy file which I then compile and include with a regular groovy include statement, I get errors. Trying to use include {MyClass} from classes.nf results in an error ERROR ~ MyClass.<init>(), while trying to use include MyClass where MyClass is compiled in a .jar file results in an error that the channel object is unknown.

Either a way of including classes defined in other .nf files, or a way of including the Nextflow dependencies like the channel object that would make it possible to include .jar classes that act on channel objects would solve my problem.

Thank you!

2

Two options here.

Firstly, you can include a Java class in the lib/ directory and it will be imported automatically. You can see that in action in the nf-core template: rnaseq/lib at master · nf-core/rnaseq · GitHub

However, for manipulating a channel you might find it easier to define a simple function which can be imported like any module or workflow: Scripts — Nextflow 23.10.1 documentation.