[
    {
        "name": "Virus_Assembler_Megahit",
        "docker_name": "virusassemblermegahit",
        "description": null,
        "version": "0.0.1",
        "author": "MBB",
        "input": "raw_reads",
        "steps": [
            {
                "title": "Quality check",
                "name": "quality_check",
                "tools": [
                    "fastqc",
                    "null"
                ],
                "default": "fastqc"
            },
            {
                "title": "Trimming",
                "name": "trimming",
                "tools": [
                    "cutadapt",
                    "trimmomatic",
                    "null"
                ],
                "default": "null"
            },
            {
                "title": "Assembling",
                "name": "assembling",
                "tools": [
                    "megahit"
                ],
                "default": "megahit"
            },
            {
                "title": "Blasting",
                "name": "blasting",
                "tools": [
                    "blastn"
                ],
                "default": "blastn"
            },
            {
                "title": "Indexing",
                "name": "indexing",
                "tools": [
                    "bwa_mem_index"
                ],
                "default": "bwa_mem_index"
            },
            {
                "title": "Mapping",
                "name": "mapping",
                "tools": [
                    "bwa_mem"
                ],
                "default": "bwa_mem"
            }
        ],
        "options": [
            {
                "name": "results_dir",
                "type": "output_dir",
                "value": "\/Results",
                "label": "Results directory: ",
                "volumes": [
                    {
                        "Results": "\/Results"
                    }
                ]
            }
        ],
        "data": [
            {
                "name": "blast_db_virus",
                "type": "directory"
            }
        ],
        "params_equals": [
            {
                "remove": "indexing__bwa_mem_index_genome_fasta"
            },
            {
                "remove": "blasting__blastn_query"
            }
        ],
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/virusassemblermegahit",
        "json": "",
        "yaml": "{\n  name: Virus_Assembler_Megahit,\n  docker_name: virusassemblermegahit,\n  description: ,\n  version: \"0.0.1\",\n  author: \"MBB\",\n  input: raw_reads,\n  steps:\n    [\n        { title: Quality check, name: quality_check, tools: [fastqc,\"null\"], default: fastqc },\n        { title: Trimming, name: trimming, tools: [cutadapt, trimmomatic, \"null\"], default: \"null\" },\n        { title: Assembling, name: assembling, tools: [megahit], default: megahit },\n        { title: Blasting, name: blasting, tools: [blastn], default: blastn },\n        { title: Indexing, name: indexing, tools: [bwa_mem_index], default: bwa_mem_index },\n        { title: Mapping, name: mapping, tools: [bwa_mem], default: bwa_mem },\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  data: [\n    {\n      name: blast_db_virus,\n      type: directory\n    }\n  ],\n  params_equals: [\n    { remove: indexing__bwa_mem_index_genome_fasta },\n    { remove: blasting__blastn_query }\n  ]\n}"
    }
]