scratch

The scratch directive executes each task in a temporary directory that is local to the compute node.

This is useful when executing tasks on an executor with a shared filesystem, because it decreases the network overhead of reading and writing files. Only the files declared as process outputs are copied to the pipeline work directory.

For example:

process hello {
    scratch true

    output:
    path 'data_out'

    script:
    """
    your_command --here
    """
}

It can also be specified in the Nextflow configuration:

process.scratch = true

By default, the scratch directive uses the $TMPDIR environment variable in the underlying node as the base scratch directory. If $TMPDIR is not defined, then it creates a scratch directory using the mktemp command.

Each task creates a subdirectory within the base scratch directory and automatically deletes it upon completion.

note

Cloud-based executors enable scratch by default since the pipeline work directory resides in object storage.

The following values are supported:

false

Do not use a scratch directory.

true

Create a scratch directory in the directory defined by the $TMPDIR environment variable, or $(mktemp /tmp) if $TMPDIR is not set.

'$YOUR_VAR'

Create a scratch directory in the directory defined by the given environment variable, or $(mktemp /tmp) if that variable is not set. The value must use single quotes, otherwise the environment variable will be evaluated in the pipeline script context.

'/my/tmp/path'

Create a scratch directory in the specified directory.

'ram-disk'

Create a scratch directory in the RAM disk /dev/shm/.