Process per file path

Problem

You need to execute a task for each file that matches a glob pattern.

Solution

Use the Channel.fromPath method to create a channel emitting all files matching the glob pattern. Then, use the channel as input of the process implementing your task.

Code

process foo {
  debug true
  input:
  path x

  script:
  """
  echo your_command --input $x
  """
}

workflow {
  foo("$baseDir/data/reads/*_1.fq.gz")
}

Run it

Use the the following command to execute the example:

nextflow run nextflow-io/patterns/process-per-file-path.nf