env

The env scope defines environment variables that are exported into the environment where tasks are executed.

Prefix each variable name with the env scope or surround them by curly brackets, as shown below:

env.ALPHA = 'some value'
env.BETA = "$HOME/some/path"

env {
     DELTA = 'one more'
     GAMMA = "/my/path:$PATH"
}

note

In the above example, variables like $HOME and $PATH are evaluated when the workflow is launched. If you want these variables to be evaluated during task execution, escape them with \$. This difference is important for variables like $PATH, which may be different in the workflow environment versus the task environment.

warning

The env scope provides environment variables to tasks, not Nextflow itself. Nextflow environment variables such as NXF_VER should be set in the environment in which Nextflow is launched.