View channel only when parameter is set

[gh-byounggreenwald]

Hi!

I am trying to do a view throughout my pipeline if I pass params.test_run as true. I like the behavior of view over dump, so prefer to do that if possible.

with just view, and some process in my workflow, the following works

process | view

this does not

process | { params.test_run ? view : map{ x -> x } }

it gives the error
Missing process or function or([Script_5fd23086685935fc$_runScript_closure7$_closure36$_closure54@137a4b54])

Lastly I would like to set this to a variable to use it in my workflow, something like

view_if_test = { params.test_run ? view : map{ x -> x } }

workflow {
process | view_if_test 
}

is this possible?

Thanks!

[bentsherman]

This should work:

process | (params.test_run ? view : map{ x -> x })

But what about view do you like over dump?

[mahesh-panchal]

You could also do it in the view operator itself.

workflow {
    Channel.of(1..3)
    | view { x -> params.debug ? x : '' }
}

[gh-byounggreenwald]

Thanks both :)

The structure of view is what i am used to looking at to track how the channel are behaving; its probably more I should just learn to examine the dump output.

I do have issues if I do dump without a tag -- from docs it seemed like this should be supported, but maybe not?

[gh-byounggreenwald]

is there a way to save this to a custom operator? should this work?

view_if_test = (params.test_run ? view : map{ x -> x })

workflow {

process | view_if_test

}

[mahesh-panchal]

You can define a function

def debug_view (ch) {
    ch | (params.test ? view : map { x -> x } )
}

workflow {
    debug_view(Channel.of(1..3))
}

Also I think it's best to use .dump with a tag. When you use --dump-channels you can leave off the arg for all channels, or you can give it a string which can also be a pattern to print one more channels.

workflow {
    Channel.of(1..3).dump(tag:'ch_numbers', pretty: true)
    Channel.of('A'..'C').dump(tag:'ch_letters')
}

nextflow run main -dump-channels
nextflow run main -dump-channels 'ch_*'
nextflow run main -dump-channels 'ch_letters'