CODEWITHSUNDEEP
workflownextflow
Valentin Ruano
Valentin Ruano

Reputation: 2809

Is there a way to provide a default value for an optional input channel?

I link to be able to do something like this:

workflow XXX {
   take:
       a
       b default ""
   main:
       if (b == "") {
          println "a is ${a} and b is unset"
       } else {
          println "a is ${a} and b is ${b}"
       }

}

However the code does not compile... what is the closest valid nextflow to that?

Upvotes: 1

Views: 1330

Answers (1)

Steve
Steve

Reputation: 54502

Workflows can declare one or more input channels using the take keyword. However, there is currently no way to modify the channels in the declaration. This usually isn't a problem though, because you can of course transform values emitted by a channel either upstream or downstream of the workflow.

I think if your workflow sometimes requires an additional input channel, then just have that workflow define that additional input channel. Then, when you call the workflow you can define a default value for the channel in the usual way - i.e. using the ifEmpty operator. For example:

nextflow.enable.dsl=2

workflow test {
   
   take:
     input_values
     input_files
   
   main:
     input_files.view()
}

workflow {

   foobarbaz = Channel.of( 'foo', 'bar', 'baz' )
   text_files = Channel.fromPath( '/path/*.txt' ).ifEmpty( file('./default.txt') )

   test( foobarbaz, text_files )
}

Alternatively, define a single input channel and use a parameter to supply a default value:

workflow test {
     
   take:
     input_values

   main:

     if( params.text_file ) {
     
       do_something( params.text_file )

     } else {

       do_something_else()
     }
}

Upvotes: 1

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