Docker permission errors

Edit

One module container fails due to Docker permissions

The nf-core template nextflow.config contains the configuration docker.runOptions = '-u $(id -u):$(id -g)' for the profiles docker and arm. This is done to emulate the user inside the container.

In some containers, this option may cause permission errors, for example when the Docker container writes to the $HOME directory, as the emulated user won’t have a $HOME directory.

One solution is to override this Docker option with a config file, with docker.runOptions = ''. However, this change will affect all the Docker containers, and can’t be overridden only in one single process. To solve this, one option is to replace docker.runOptions and use containerOptions instead.

Your new nextflow.config file should look like this:

profiles {
  docker {
    process.containerOptions = '-u $(id -u):$(id -g)'
  }
  arm {
    process.containerOptions = '-u $(id -u):$(id -g)'
  }
}

And you can override this value for a particular process selecting it by name, in the modules.config file:

process {
  withName: <TOOL> {
        containerOptions = ''
    }
}