Docker containers

Nextflow integration with Docker containers technology allows you to write self-contained and truly reproducible computational pipelines.

By using this feature any process in a Nextflow script can be transparently executed into a Docker container. This may be extremely useful to package the binary dependencies of a script into a standard and portable format that can be executed on any platform supporting the Docker engine.

Prerequisites

You will need Docker installed on your execution environment e.g. your computer or a distributed cluster, depending on where you want to run your pipeline.

If you are running Docker on Mac OSX make sure you are mounting your local /Users directory into the Docker VM as explained in this excellent tutorial: How to use Docker on OSX.

How it works

You won't need to modify your Nextflow script in order to run it with Docker. Simply specify the Docker image from where the containers are started by using the -with-docker command line option. For example:

nextflow run <your script> -with-docker [docker image]

Every time your script launches a process execution, Nextflow will run it into a Docker container created by using the specified image. In practice Nextflow will automatically wrap your processes and run them by executing the docker run command with the image you have provided.

Note

A Docker image can contain any tool or piece of software you may need to carry out a process execution. Moreover the container is run in such a way that the process result files are created in the hosting file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.

If you want to avoid entering the Docker image as a command line parameter, you can define it in the Nextflow configuration file. For example you can add the following lines in the nextflow.config file:

process.container = 'nextflow/examples:latest'
docker.enabled = true

In the above example replace nextflow/examples:latest with any Docker image of your choice.

Read the Configuration page to learn more about the nextflow.config file and how to use it to configure your pipeline execution.

Warning

Nextflow automatically manages the file system mounts each time a container is launched depending on the process input files. Note, however, that when a process input is a symbolic link file, the linked file must be stored in the same folder where the symlink is located, or any its sub-folder. Otherwise the process execution will fail because the launched container won't be able to access the linked file.

Multiple containers

It is possible to specify a different Docker image for each process definition in your pipeline script. Let's suppose you have two processes named foo and bar. You can specify two different Docker images for them in the Nextflow script as shown below:

process foo {
  container 'image_name_1'

  '''
  do this
  '''
}

process bar {
  container 'image_name_2'

  '''
  do that
  '''
}

Alternatively, the same containers definitions can be provided by using the nextflow.config file as shown below:

process.$foo.container = 'image_name_1'
process.$bar.container = 'image_name_2'
docker.enabled = true

Read the Process scope section to learn more about processes configuration.

Executable containers

An executable container is a Docker image which defines a command entry point i.e. a command that is executed by default when the container start.

In order to use an executable container with Nextflow set the process' directive container to the value true and use the Docker image name (including the user/organisation name) as the first command in the process script, followed eventually by any command parameters.

For example:

process runImage {
  container true

  '''
  docker/image --foo --bar
  '''

}

The docker image name can be preceded by one or more lines containing comments or variables definition i.e. NAME=VALUE and can be followed by one or more lines containing BASH commands.

Warning

This is an experimental feature. It may change in future Nextflow releases.

Advanced settings

Docker advanced configuration settings are described in Scope docker section in the Nextflow configuration page.