Process inclusion warnings

[yashpatel6]

With the update to Nextflow version 22.10.2, it looks like having something like:

include { val_process; val_process as val_process_output } from './validation.nf'

gives a WARN message that val_process_output is defined more than once.

To fix, each process instance needs to be named:

include { val_process as val_process_input; val_process as val_process_output } from './validation.nf'