CLI reference

The Nextflow CLI takes top-level options, a command, and the command's arguments:

$ nextflow [options] COMMAND [arg...]

Options apply to every command. Each command has its own reference page with usage, options, subcommands, and examples.

Options

Option	Description
`-C`	Comma-separated list of configuration files to use as the configuration set. Nextflow ignores all default configuration files.
`-D`	Set JVM properties, for example `-Dfile.encoding=UTF-8`. Equivalent to the `NXF_JVM_ARGS` environment variable.
`-bg`	Run Nextflow in the background. You can close your terminal without terminating the pipeline run.
`-c, -config`	Comma-separated list of configuration files to add to the configuration set.
`-h`	Print available commands and options.
`-log`	Set Nextflow log file path (default: `.nextflow.log`). Must be a local path.
`-q, -quiet`	Do not print the Nextflow banner and execution progress to the console. Does not affect error messages.
`-remote-debug`	Enable JVM interactive remote debugging (experimental).
`-syslog`	Send logs to a Syslog server, for example `localhost:514`.
`-trace`	Enable trace level logging for the specified packages. Separate multiple packages with a comma, for example `-trace nextflow,io.seqera`.
`-v, -version`	Print the program version.

Command	Description
`auth`	Manage Seqera Platform authentication.
`clean`	Clean up cache and work directories.
`clone`	Clone a remote project into a folder.
`config`	Print the resolved pipeline configuration.
`console`	Launch the Nextflow interactive console.
`drop`	Delete the local copy of a project.
`fs`	Perform basic filesystem operations.
`help`	Print the top-level help or specific help for a command.
`info`	Print project or system runtime information.
`inspect`	Inspect process settings in a pipeline project.
`kuberun`	Launch a Nextflow pipeline on a Kubernetes cluster.
`launch`	Launch a workflow in Seqera Platform.
`lineage`	Inspect lineage metadata for Nextflow runs.
`lint`	Lint Nextflow scripts and config files.
`list`	List all downloaded projects.
`log`	Print the execution history and log information.
`logfile`	Print the contents of a Nextflow log file.
`module`	Manage Nextflow modules.
`plugin`	Manage plugins and run plugin-specific commands.
`pull`	Download or update a project.
`run`	Execute a pipeline.
`secrets`	Manage pipeline secrets.
`self-update`	Update the Nextflow runtime to the latest available version.
`view`	View a project's script file(s).