optional-input.adoc

Optional input

Problem

One or more processes have an optional input file.

Solution

Use a special file name to mark the absence of the file parameter.

Code

params.inputs = 'prots/*{1,2,3}.fa'
params.filter = 'NO_FILE'

prots_ch = Channel.fromPath(params.inputs)
opt_file = file(params.filter)

process foo {
  input:
  file seq from prots_ch
  file opt from opt_file

  script:
  def filter = opt.name != 'NO_FILE' ? "--filter $opt" : ''
  """
  your_commad --input $seq $filter
  """
}

Run it

Run the script with the following command:

nextflow run patterns/optional-input.nf

Run the same script providing an optional file input:

nextflow run patterns/optional-input.nf --filter foo.txt