[
    {
        "name": "RNAseq_denovo",
        "docker_name": "rnaseqdenovo",
        "description": null,
        "version": "0.0.1",
        "author": "MBB",
        "input": "raw_reads",
        "steps": [
            {
                "title": "Trimming",
                "name": "trimming",
                "tools": [
                    "trimmomatic",
                    "null"
                ],
                "default": "null"
            },
            {
                "title": "Quality check",
                "name": "quality_check",
                "tools": [
                    "fastqc"
                ],
                "default": "fastqc"
            },
            {
                "title": "Assembling",
                "name": "assembling",
                "tools": [
                    "trinity"
                ],
                "default": "trinity"
            },
            {
                "title": "Evaluate assembling",
                "name": "evaluate_assembling",
                "tools": [
                    "transrate"
                ],
                "default": "transrate"
            },
            {
                "title": "Protein coding domains prediction",
                "name": "prot_domains_pred",
                "tools": [
                    "transdecoder"
                ],
                "default": "transdecoder"
            },
            {
                "title": "Functional annotation",
                "name": "funct_annot",
                "tools": [
                    "interproscan"
                ],
                "default": "interproscan"
            }
        ],
        "options": [
            {
                "name": "results_dir",
                "type": "output_dir",
                "value": "\/Results",
                "label": "Results directory: ",
                "volumes": [
                    {
                        "Results": "\/Results"
                    }
                ]
            }
        ],
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/rnaseqdenovo",
        "json": "",
        "yaml": "{\n  name: RNAseq_denovo,\n  docker_name: rnaseqdenovo,\n  description: ,\n  version: \"0.0.1\",\n  author: \"MBB\",\n  input: raw_reads,\n  steps:\n    [\n        { title: Trimming, name: trimming, tools: [trimmomatic, \"null\"], default: \"null\" },\n        { title: Quality check, name: quality_check, tools: [fastqc], default: fastqc },\n        { title: Assembling, name: assembling, tools: [trinity], default: trinity },\n        { title: Evaluate assembling, name: evaluate_assembling, tools: [transrate], default: transrate },\n        { title: Protein coding domains prediction, name: prot_domains_pred, tools: [transdecoder], default: transdecoder },\n        { title: Functional annotation, name: funct_annot, tools: [interproscan], default: interproscan }\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}"
    }
]