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scratch

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

Usage​

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
    """
}

You can also set it 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 because the pipeline work directory resides in object storage.

Options​

The following values are available:

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 is 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/.

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