---
title: CLI reference
description: Reference for the top-level Nextflow CLI options and commands.
---

# CLI reference

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

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

[Options](#options) apply to every command. Each [command](#commands) 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. |
| <code style={{whiteSpace: 'nowrap'}}>-remote-debug</code> | Enable JVM interactive remote debugging (experimental). |
| `-syslog` | Send logs to a [Syslog](https://en.wikipedia.org/wiki/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. |


## Commands

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

[cli-page]: ../cli
[cli-auth]: ./cli/auth
[cli-clean]: ./cli/clean
[cli-clone]: ./cli/clone
[cli-config]: ./cli/config
[cli-console]: ./cli/console
[cli-drop]: ./cli/drop
[cli-fs]: ./cli/fs
[cli-help]: ./cli/help
[cli-info]: ./cli/info
[cli-inspect]: ./cli/inspect
[cli-kuberun]: ./cli/kuberun
[cli-launch]: ./cli/launch
[cli-lineage]: ./cli/lineage
[cli-lint]: ./cli/lint
[cli-list]: ./cli/list
[cli-log]: ./cli/log
[cli-logfile]: ./cli/logfile
[cli-module]: ./cli/module
[cli-plugin]: ./cli/plugin
[cli-pull]: ./cli/pull
[cli-run]: ./cli/run
[cli-secrets]: ./cli/secrets
[cli-self-update]: ./cli/self-update
[cli-view]: ./cli/view
