[
    {
        "name": "MitoZ",
        "docker_name": "mitoz",
        "description": null,
        "version": "0.0.1",
        "author": "MBB",
        "input": "raw_reads",
        "steps": [
            {
                "title": "Trimming",
                "name": "trimming",
                "tools": [
                    "cutadapt",
                    "null"
                ],
                "default": "null"
            },
            {
                "title": "Filter",
                "name": "filter",
                "tools": [
                    "mitoz_filter",
                    "null"
                ],
                "default": "mitoz_filter"
            },
            {
                "title": "Assemble",
                "name": "assemble",
                "tools": [
                    "mitoz_assemble"
                ],
                "default": "mitoz_assemble"
            },
            {
                "title": "Annotate",
                "name": "annotate",
                "tools": [
                    "mitoz_annotate"
                ],
                "default": "mitoz_annotate"
            },
            {
                "title": "Visualize",
                "name": "visualize",
                "tools": [
                    "igv_visualize"
                ],
                "default": "igv_visualize"
            }
        ],
        "options": [
            {
                "name": "results_dir",
                "type": "output_dir",
                "value": "\/Results",
                "label": "Results directory: ",
                "volumes": [
                    {
                        "Results": "\/Results"
                    }
                ]
            }
        ],
        "params_equals": [
            {
                "param_A": "assemble__mitoz_assemble_clade",
                "param_B": "annotate__mitoz_annotate_clade"
            }
        ],
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/mitoz",
        "json": "",
        "yaml": "{\n  name: MitoZ,\n  docker_name: mitoz,\n  description: ,\n  version: \"0.0.1\",\n  author: \"MBB\",\n  input: raw_reads,\n  steps:\n    [\n      { title: Trimming, name: trimming, tools: [cutadapt, \"null\"], default: \"null\" },\n      { title: Filter, name: filter, tools: [mitoz_filter,\"null\"], default: mitoz_filter},\n      { title: Assemble, name: assemble, tools: [mitoz_assemble], default: mitoz_assemble}, # Runs mitoz_findmitoscaf after assembling\n      #{ title: Find Mito scaffold, name: findmitoscaf, tools: [mitoz_findmitoscaf], default: mitoz_findmitoscaf},\n      { title: Annotate, name: annotate, tools: [mitoz_annotate], default: mitoz_annotate}, # Runs mitoz_visualize after annotating\n      { title: Visualize, name: visualize, tools: [igv_visualize], default: igv_visualize },\n    ],\n  options:\n    [\n      {\n        name: \"results_dir\",\n        type: \"output_dir\",\n        value: \"\/Results\",\n        label: \"Results directory: \",\n        volumes:  [Results: \"\/Results\"]\n      },\n    ],\n    params_equals: [\n      { param_A: assemble__mitoz_assemble_clade, param_B: annotate__mitoz_annotate_clade },\n    ]\n}"
    }
]