no_container_per_process.md

Run some processes outside containers

As you're probably aware, you can tell Nextflow to run processes instances in containers by simply setting the container process directive and enabling your container technology of choice. For example, in your nextflow.config, add the following:

docker.enabled = true

Then create a pipeline script with the following:

process FOO {
  container 'nextflow/rnaseq-nf'

  output:
  path 'salmon_version'

  """
  salmon --version > salmon_version
  """
}

workflow {
  FOO()
}

In the snippet above, we're basically saving the version of the salmon software to a file named salmon_version. We also told Nextflow to run this task inside a container created with the image rnaseq-nf in the nextflow namespace. Because we didn't say where, Nextflow will look in Docker Hub by default, but you could also specify other container registries such as Quay.io.

So, in an hypothetical scenario, you want to have your tasks run in containers with Docker but there is one specific process whose tasks are very lightweight and free of dependencies. How do you tell Nextflow to run these tasks locally? You set the container process directive to an empty string or false. See the example below:

process FOO {
  container ''

  output:
  path 'salmon_version'

  """
  salmon --version > salmon_version
  """
}

workflow {
  FOO()
}

As you can see, it's basically a matter of setting the container process directive to an empty string (or false).