process-per-file-path.adoc

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

Channel.fromPath('reads/*_1.fq.gz').set{ samples_ch }

process foo {
  input:
  file x from samples_ch

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

Run it

Use the the following command to execute the example:

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