shell

The shell directive defines a custom shell command for process scripts. By default, script blocks are executed with /bin/bash -ue.

Usage

For example:

process hello {
    shell '/bin/bash', '-euo', 'pipefail'

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

You can also set it in the Nextflow configuration:

process.shell = ['/bin/bash', '-euo', 'pipefail']