{
  "description": "Run or preview a Snakefile workflow. Cluster, container, conda, report and plugin options are left out.",
  "options": [
    {
      "names": [
        "--cores",
        "-j"
      ],
      "description": "Maximum cores in parallel.",
      "args": {
        "name": "cores",
        "description": "Maximum cores in parallel.",
        "isOptional": false
      }
    },
    {
      "names": [
        "--snakefile",
        "-s"
      ],
      "description": "Snakefile",
      "args": {
        "name": "snakefile",
        "isOptional": false,
        "template": "filepaths"
      }
    },
    {
      "names": [
        "--configfile"
      ],
      "description": "Config file",
      "args": {
        "name": "configfile",
        "isOptional": false,
        "template": "filepaths"
      }
    },
    {
      "names": [
        "--directory",
        "-d"
      ],
      "description": "Working directory",
      "args": {
        "name": "directory",
        "isOptional": false,
        "template": "folders"
      }
    },
    {
      "names": [
        "--dryrun",
        "-n"
      ],
      "description": "Dry run"
    },
    {
      "names": [
        "--printshellcmds",
        "-p"
      ],
      "description": "Print shell commands"
    },
    {
      "names": [
        "--reason",
        "-r"
      ],
      "description": "Print reason for each job"
    },
    {
      "names": [
        "--keep-going",
        "-k"
      ],
      "description": "Keep going after failures"
    },
    {
      "names": [
        "--forceall",
        "-F"
      ],
      "description": "Force re-run of all dependencies",
      "isDangerous": true
    },
    {
      "names": [
        "--rerun-incomplete",
        "--ri"
      ],
      "description": "Re-run incomplete jobs"
    },
    {
      "names": [
        "--unlock"
      ],
      "description": "Remove working directory lock"
    },
    {
      "names": [
        "--list",
        "-l"
      ],
      "description": "List rules"
    },
    {
      "names": [
        "--dag"
      ],
      "description": "Print the job DAG (dot)"
    }
  ],
  "args": [
    {
      "name": "targets",
      "description": "Rules or files to build. Empty builds the first rule.",
      "isOptional": true,
      "isVariadic": true
    }
  ],
  "name": "snakemake"
}