{
  "id": "nextflow",
  "name": "Nextflow",
  "homepage": "https://www.nextflow.io",
  "description": "Nextflow is a workflow system for creating scalable, portable, and reproducible workflows.",
  "icon": "SimpleIcons:nextflow",
  "executables": [
    "nextflow"
  ],
  "dotfiles": {
    "paths": [
      "~/.nextflow/config"
    ],
    "exclude": [],
    "secret": [
      "~/.nextflow/scm"
    ]
  },
  "commands": {
    "format": 1,
    "label": "Nextflow",
    "description": "Global options only; use the Run and Pull subcommands.",
    "quality": "ai-draft",
    "base": "fig:nextflow",
    "parser": {
      "end_of_options": "--",
      "interleave": "permute",
      "long_equals": false,
      "short_attached": false,
      "short_bundles": false
    },
    "source": [
      {
        "id": "fig",
        "kind": "completion",
        "url": "https://github.com/withfig/autocomplete/blob/master/src/nextflow.ts",
        "license": "MIT"
      }
    ],
    "subcommand": [
      {
        "path": [
          "run"
        ],
        "label": "Run pipeline",
        "description": "Execute a pipeline project. Docker image arguments, env/process overrides and container runtimes besides Docker are left out.",
        "source": [
          {
            "id": "fig",
            "kind": "completion",
            "url": "https://github.com/withfig/autocomplete/blob/master/src/nextflow.ts",
            "license": "MIT"
          }
        ],
        "field": [
          {
            "id": "pipeline",
            "label": "Pipeline (name, URL or path)",
            "type": "string",
            "position": 0,
            "sources": [
              "fig"
            ]
          },
          {
            "id": "revision",
            "label": "Revision",
            "type": "string",
            "option": [
              "-r",
              "-revision"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "profile",
            "label": "Profile",
            "type": "string",
            "option": [
              "-profile"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "params_file",
            "label": "Params file (JSON/YAML)",
            "type": "path",
            "option": [
              "-params-file"
            ],
            "path": {
              "kind": "file",
              "role": "input"
            },
            "sources": [
              "fig"
            ]
          },
          {
            "id": "work_dir",
            "label": "Work directory",
            "type": "path",
            "option": [
              "-w",
              "-work-dir"
            ],
            "path": {
              "kind": "directory",
              "role": "input"
            },
            "sources": [
              "fig"
            ]
          },
          {
            "id": "name",
            "label": "Run name",
            "type": "string",
            "option": [
              "-name"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "resume",
            "label": "Resume cached run",
            "type": "boolean",
            "option": [
              "-resume"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "with_docker",
            "label": "Run with Docker",
            "type": "boolean",
            "option": [
              "-with-docker"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "with_report",
            "label": "HTML report file",
            "type": "path",
            "option": [
              "-with-report"
            ],
            "path": {
              "kind": "file",
              "role": "output"
            },
            "sources": [
              "fig"
            ]
          },
          {
            "id": "with_trace",
            "label": "Trace file",
            "type": "path",
            "option": [
              "-with-trace"
            ],
            "path": {
              "kind": "file",
              "role": "output"
            },
            "sources": [
              "fig"
            ]
          },
          {
            "id": "with_timeline",
            "label": "Timeline file",
            "type": "path",
            "option": [
              "-with-timeline"
            ],
            "path": {
              "kind": "file",
              "role": "output"
            },
            "sources": [
              "fig"
            ]
          },
          {
            "id": "stub",
            "label": "Stub run",
            "type": "boolean",
            "option": [
              "-stub"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "latest",
            "label": "Pull latest first",
            "type": "boolean",
            "option": [
              "-latest"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "offline",
            "label": "Offline",
            "type": "boolean",
            "option": [
              "-offline"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "queue_size",
            "label": "Queue size",
            "type": "integer",
            "option": [
              "-qs",
              "-queue-size"
            ],
            "sources": [
              "fig"
            ]
          }
        ],
        "task": [
          {
            "id": "run",
            "label": "Run pipeline",
            "fields": [
              "pipeline",
              "revision",
              "profile",
              "params_file",
              "work_dir"
            ],
            "required": [
              "pipeline"
            ]
          },
          {
            "id": "resume",
            "label": "Resume last run",
            "fields": [
              "pipeline",
              "profile",
              "params_file"
            ],
            "required": [
              "pipeline"
            ],
            "set": {
              "resume": [
                true
              ]
            }
          }
        ],
        "group": [
          {
            "id": "basic",
            "label": "Basic",
            "fields": [
              "pipeline",
              "revision",
              "profile",
              "params_file",
              "work_dir",
              "resume",
              "with_docker"
            ]
          },
          {
            "id": "advanced",
            "label": "Advanced",
            "fields": [
              "name",
              "with_report",
              "with_trace",
              "with_timeline",
              "stub",
              "latest",
              "offline",
              "queue_size"
            ]
          }
        ]
      },
      {
        "path": [
          "pull"
        ],
        "label": "Pull project",
        "description": "Download or update a project.",
        "source": [
          {
            "id": "fig",
            "kind": "completion",
            "url": "https://github.com/withfig/autocomplete/blob/master/src/nextflow.ts",
            "license": "MIT"
          }
        ],
        "field": [
          {
            "id": "project",
            "label": "Project name or URL",
            "type": "string",
            "position": 0,
            "sources": [
              "fig"
            ]
          },
          {
            "id": "revision",
            "label": "Revision",
            "type": "string",
            "option": [
              "-r",
              "-revision"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "all",
            "label": "Update all projects",
            "type": "boolean",
            "option": [
              "-all"
            ],
            "sources": [
              "fig"
            ]
          },
          {
            "id": "user",
            "label": "Username",
            "type": "string",
            "option": [
              "-user"
            ],
            "sources": [
              "fig"
            ]
          }
        ],
        "task": [
          {
            "id": "pull",
            "label": "Pull project",
            "fields": [
              "project",
              "revision"
            ],
            "required": [
              "project"
            ]
          },
          {
            "id": "pull-all",
            "label": "Update all",
            "fields": [
              "all"
            ],
            "required": [],
            "set": {
              "all": [
                true
              ]
            }
          }
        ],
        "group": [
          {
            "id": "basic",
            "label": "Basic",
            "fields": [
              "project",
              "revision",
              "all"
            ]
          },
          {
            "id": "advanced",
            "label": "Advanced",
            "fields": [
              "user"
            ]
          }
        ]
      }
    ]
  }
}