optional-input.md

Problem

One or more processes have an optional input file.

Solution

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

Create an empty file in assets:

touch assets/NO_FILE

Code

params.inputs = "$projectDir/data/prots/*{1,2,3}.fa"
params.filter = "$projectDir/assets/NO_FILE"

process foo {
  debug true
  input:
  path seq
  path opt

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

workflow {
  prots_ch = Channel.fromPath(params.inputs, checkIfExists:true)
  opt_file = file(params.filter, checkIfExists:true)

  foo(prots_ch, opt_file)
}

Run it

Run the script with the following command:

nextflow run nextflow-io/patterns/optional-input.nf 

Run the same script providing an optional file input:

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