Setting variable from inside (non-groovy) script

[Robert Syme]

Hi all

I'd like a process that takes a single input and returns a set of two elements; an id (determined by a script) and an output file. At the moment, I've got a process that outputs the file using the id in the filename. The channel is then mapped to split the id from the file:

process example {

  input:

  val foo from example_in

  output:

  'file.txt' into example_out

  """

id=`get_id $foo`

get_file $foo > \$id.txt

"""

}

example_out.map{  out_file -> [out_file.getBaseName(), out_file]

Is there a better way of writing a process that takes a single value and then outputs a set of val, file where the val is the output of a script?

Thanks!

[Paolo Di Tommaso]

Hi Robert, 

A slightly better workaround is using the stdout output to capture the BASH variable value. Something like the following: 

process example {

  input:

  val foo from 2

  output:

  set stdout, file('file.txt') into example_out

  """

  id=`get_id $foo`

  echo $foo > file.txt

  printf "$foo"

  """

}

However I agree that should be a more specific mechanism to capture the BASH variable as output values. 

Would you like to open a feature request for this? 

Cheers,

Paolo

  

 

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[Rob Syme]

Thanks Paolo

I think that in most cases, users will need to extract only a single ID variable, in which case the stdout solution is sufficient. I've opened an issue in case others would like a more complete solution.

-r

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[Rob Syme]

Discussion continued at github.com/nextflow-io/nextflow/issues/69