[
    {
        "name": "Genome_Profile",
        "docker_name": "genomeprofiler",
        "description": "Infer the global properties of a genome from unassembled sequenced data",
        "version": "0.0.1",
        "author": "MBB",
        "input": "raw_reads",
        "steps": [
            {
                "title": "Preprocessing",
                "name": "preprocessing",
                "tools": [
                    "fastp",
                    "null"
                ],
                "default": "null"
            },
            {
                "title": "K-mer counting",
                "name": "kmer_counting",
                "tools": [
                    "jellyfish_count"
                ],
                "default": "jellyfish_count"
            },
            {
                "title": "K-mer histogram",
                "name": "kmer_histogram",
                "tools": [
                    "jellyfish_histo"
                ],
                "default": "jellyfish_histo"
            },
            {
                "title": "K-mer analysis",
                "name": "kmer_analysis",
                "tools": [
                    "genomescope"
                ],
                "default": "genomescope"
            }
        ],
        "options": [
            {
                "name": "results_dir",
                "type": "output_dir",
                "value": "\/Results",
                "label": "Results directory: ",
                "volumes": [
                    {
                        "Results": "\/Results"
                    }
                ]
            }
        ],
        "steps_in": [
            {
                "step_name": "preprocessing",
                "tool_name": "fastp",
                "rule_name": "fastp_PE",
                "params": [
                    {
                        "input_name": "read",
                        "origin_step": "",
                        "origin_command": "raw_reads",
                        "origin_name": "read"
                    },
                    {
                        "input_name": "read2",
                        "origin_step": "",
                        "origin_command": "raw_reads",
                        "origin_name": "read2"
                    }
                ]
            },
            {
                "step_name": "preprocessing",
                "tool_name": "fastp",
                "rule_name": "fastp_SE",
                "params": [
                    {
                        "input_name": "read",
                        "origin_step": "",
                        "origin_command": "raw_reads",
                        "origin_name": "read_preprocessed"
                    }
                ]
            },
            {
                "step_name": "kmer_counting",
                "tool_name": "jellyfish_count",
                "rule_name": "jellyfish_count",
                "params": [
                    {
                        "input_name": "read",
                        "origin_step": "",
                        "origin_command": "raw_reads",
                        "origin_name": "read"
                    },
                    {
                        "input_name": "read2",
                        "origin_step": "",
                        "origin_command": "raw_reads",
                        "origin_name": "read2"
                    },
                    {
                        "input_name": "read",
                        "origin_step": "preprocessing",
                        "origin_command": "fastp_PE",
                        "origin_name": "read_preprocessed"
                    },
                    {
                        "input_name": "read2",
                        "origin_step": "preprocessing",
                        "origin_command": "fastp_PE",
                        "origin_name": "read2_preprocessed"
                    }
                ]
            },
            {
                "step_name": "kmer_histogram",
                "tool_name": "jellyfish_histo",
                "rule_name": "jellyfish_histo",
                "params": [
                    {
                        "input_name": "kmer_counts",
                        "origin_step": "kmer_counting",
                        "origin_command": "jellyfish_count",
                        "origin_name": "kmer_counts"
                    }
                ]
            },
            {
                "step_name": "kmer_analysis",
                "tool_name": "genomescope",
                "rule_name": "genomescope",
                "params": [
                    {
                        "input_name": "kmer_histo",
                        "origin_step": "kmer_histogram",
                        "origin_command": "jellyfish_histo",
                        "origin_name": "kmer_histo"
                    }
                ]
            }
        ],
        "params_equals": [
            {
                "param_A": "kmer_counting__jellyfish_count_kmer_len",
                "param_B": "kmer_analysis__genomescope_kmer_len"
            }
        ],
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/genomeprofiler",
        "json": "",
        "yaml": "{\n  name: Genome_Profile,\n  docker_name: genomeprofiler,\n  description: \"Infer the global properties of a genome from unassembled sequenced data\",\n  version: \"0.0.1\",\n  author: \"MBB\",\n  input: raw_reads,\n  steps:\n    [\n      { title: Preprocessing, name: preprocessing, tools: [fastp,\"null\"], default: \"null\" },\n      { title: K-mer counting, name: kmer_counting, tools: [jellyfish_count], default: jellyfish_count },\n      { title: K-mer histogram, name: kmer_histogram, tools: [jellyfish_histo], default: jellyfish_histo },\n      { title: K-mer analysis, name: kmer_analysis, tools: [genomescope], default: genomescope },\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    steps_in: [\n      { step_name: preprocessing, tool_name: fastp, rule_name: fastp_PE, \n        params: [ \n          {input_name: read, origin_step: \"\", origin_command: raw_reads, origin_name: read },\n          {input_name: read2, origin_step: \"\", origin_command: raw_reads, origin_name: read2 }\n        ]\n      },\n      { step_name: preprocessing, tool_name: fastp, rule_name: fastp_SE, \n        params: [ \n          {input_name: read, origin_step: \"\", origin_command: raw_reads, origin_name: read_preprocessed },\n        ]\n      },\n      { step_name: kmer_counting, tool_name: jellyfish_count, rule_name: jellyfish_count, \n        params: [ \n          {input_name: read, origin_step: \"\", origin_command: raw_reads, origin_name: read },\n          {input_name: read2, origin_step: \"\", origin_command: raw_reads, origin_name: read2 },\n          {input_name: read, origin_step: \"preprocessing\", origin_command: fastp_PE, origin_name: read_preprocessed },\n          {input_name: read2, origin_step: \"preprocessing\", origin_command: fastp_PE, origin_name: read2_preprocessed },\n        ]\n      },\n      { step_name: kmer_histogram, tool_name: jellyfish_histo, rule_name: jellyfish_histo, \n        params: [ \n          {input_name: kmer_counts, origin_step: \"kmer_counting\", origin_command: jellyfish_count, origin_name: kmer_counts },\n        ]\n      },\n      { step_name: kmer_analysis, tool_name: genomescope, rule_name: genomescope, \n        params: [ \n          {input_name: kmer_histo, origin_step: \"kmer_histogram\", origin_command: jellyfish_histo, origin_name: kmer_histo },\n        ]\n      },\n    ],\n    params_equals: [\n      { param_A: kmer_counting__jellyfish_count_kmer_len, param_B: kmer_analysis__genomescope_kmer_len },\n    ]\n}"
    }
]