{
  "name": "nextflow",
  "path": "nextflow",
  "usage": "nextflow [options] COMMAND [arg...]",
  "params": [
    {"name": "config", "kind": "option", "type": "List", "opts": ["-C"], "help": "Use the specified configuration file(s) overriding any defaults"},
    {"name": "jvmOpts", "kind": "option", "type": "Map", "opts": ["-D"], "help": "Set JVM properties"},
    {"name": "background", "kind": "option", "type": "boolean", "opts": ["-bg"], "help": "Execute nextflow in background", "is_flag": true},
    {"name": "userConfig", "kind": "option", "type": "List", "opts": ["-c", "-config"], "help": "Add the specified file to configuration set"},
    {
      "name": "ignoreConfigIncludes",
      "kind": "option",
      "type": "boolean",
      "opts": ["-config-ignore-includes"],
      "help": "Disable the parsing of config includes",
      "is_flag": true
    },
    {"name": "debug", "kind": "option", "type": "List", "opts": ["-debug"], "hidden": true},
    {"name": "logFile", "kind": "option", "type": "String", "opts": ["-log"], "help": "Set nextflow log file path"},
    {"name": "quiet", "kind": "option", "type": "boolean", "opts": ["-q", "-quiet"], "help": "Do not print information messages", "is_flag": true},
    {
      "name": "remoteDebug",
      "kind": "option",
      "type": "boolean",
      "opts": ["-remote-debug"],
      "help": "Enable JVM interactive remote debugging (experimental)",
      "is_flag": true
    },
    {
      "name": "selfUpdate",
      "kind": "option",
      "type": "boolean",
      "opts": ["-self-update"],
      "help": "Update nextflow to the latest version",
      "is_flag": true,
      "hidden": true
    },
    {"name": "syslog", "kind": "option", "type": "String", "opts": ["-syslog"], "help": "Send logs to syslog server (eg. localhost:514)"},
    {
      "name": "trace",
      "kind": "option",
      "type": "List",
      "opts": ["-trace"],
      "help": "Enable trace level logging for the specified package name - multiple packages can be provided separating them with a comma e.g. '-trace nextflow,io.seqera'"
    },
    {"name": "version", "kind": "option", "type": "boolean", "opts": ["-v", "-version"], "help": "Print the program version", "is_flag": true}
  ],
  "subcommands": {
    "auth": {
      "help": "Manage Seqera Platform authentication",
      "subcommands": {
        "config": {"help": "Configure Seqera Platform settings"},
        "login": {"help": "Authenticate with Seqera Platform"},
        "logout": {"help": "Remove authentication and revoke access token"},
        "status": {"help": "Show current authentication status and configuration"}
      }
    },
    "clean": {"help": "Clean up project cache and work directories"},
    "clone": {"help": "Clone a project into a folder"},
    "config": {"help": "Print a project configuration"},
    "console": {"help": "Launch Nextflow interactive console"},
    "drop": {"help": "Delete the local copy of a project"},
    "fs": {
      "help": "Perform filesystem operations",
      "subcommands": {
        "cat": {"help": "Print a file to the stdout"},
        "cp": {"help": "Copy a file"},
        "ls": {"help": "List the content of a folder"},
        "mv": {"help": "Move a file"},
        "rm": {"help": "Remove a file"},
        "stat": {"help": "Print file to meta info"}
      }
    },
    "help": {"help": "Print the usage help for a command"},
    "info": {"help": "Print project and system runtime information"},
    "inspect": {"help": "Inspect process settings in a pipeline project"},
    "kuberun": {"help": "Execute a workflow in a Kubernetes cluster (experimental)"},
    "launch": {"help": "Launch a workflow in Seqera Platform"},
    "lineage": {
      "help": "Explore workflows lineage metadata",
      "subcommands": {
        "check": {"help": "Checks the integrity of an lineage file path"},
        "diff": {"help": "Show differences between two lineage descriptions"},
        "find": {"help": "Find lineage metadata descriptions matching with a query"},
        "list": {"help": "List the executions with lineage enabled"},
        "render": {"help": "Render the lineage graph for a workflow output"},
        "view": {"help": "Print the description of a Lineage ID (lid)"}
      }
    },
    "lint": {"help": "Lint Nextflow scripts and config files"},
    "list": {"help": "List all downloaded projects"},
    "log": {"help": "Print executions log and runtime info"},
    "logfile": {"help": "Print the contents of a Nextflow log file"},
    "module": {
      "help": "Manage Nextflow modules",
      "subcommands": {
        "create": {"help": "Create a new module skeleton"},
        "install": {"help": "Install a module from the registry"},
        "list": {"help": "List all installed modules"},
        "publish": {"help": "Publish a module to the registry"},
        "remove": {"help": "Remove an installed module"},
        "run": {"help": "Run a module directly from the registry"},
        "search": {"help": "Search for modules in the registry"},
        "spec": {"help": "Generate a meta.yml spec for a local module"},
        "validate": {"help": "Validate a module structure and metadata"},
        "view": {"help": "Show module information and usage template"}
      }
    },
    "plugin": {
      "help": "Execute plugin-specific commands",
      "subcommands": {"create": {"help": "Create a new plugin project from the template"}, "install": {"help": "Install a plugin"}}
    },
    "pull": {"help": "Download or update a project"},
    "run": {"help": "Execute a pipeline project"},
    "secrets": {
      "help": "Manage pipeline secrets",
      "subcommands": {
        "delete": {"help": "Delete an entry from the secrets store"},
        "get": {"help": "Get a secret value with the name"},
        "list": {"help": "List all names in the secrets store"},
        "set": {"help": "Set a key-pair in the secrets store"}
      }
    },
    "self-update": {"help": "Update nextflow runtime to the latest available version"},
    "view": {"help": "View project script file(s)"}
  }
}