[
    {
        "name": "RNAseq",
        "docker_name": "rnaseqde",
        "description": "Differential expression from RNAseq counts",
        "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",
                    "null"
                ],
                "default": "fastqc"
            },
            {
                "title": "Indexing",
                "name": "indexing",
                "tools": [
                    "kallisto_index",
                    "salmon_index"
                ],
                "default": "kallisto_index"
            },
            {
                "title": "Quantification",
                "name": "quantification",
                "tools": [
                    "kallisto",
                    "salmon"
                ],
                "default": "kallisto"
            },
            {
                "title": "Differential expression",
                "name": "DE",
                "tools": [
                    "edger",
                    "deseq2"
                ],
                "default": "edger"
            }
        ],
        "options": [
            {
                "name": "results_dir",
                "type": "output_dir",
                "value": "\/Results",
                "label": "Results directory: ",
                "volumes": [
                    {
                        "Results": "\/Results"
                    }
                ]
            },
            {
                "name": "group_file",
                "type": "input_file",
                "value": "",
                "label": "Group file (TSV with col1(sample name), col2 (group)): "
            }
        ],
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/rnaseqde",
        "json": "",
        "yaml": "{\n  name: RNAseq,\n  docker_name: rnaseqde,\n  description: Differential expression from RNAseq counts,\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, \"null\"], default: fastqc },\n        { title: Indexing, name: indexing, tools: [kallisto_index, salmon_index], default: kallisto_index },\n        { title: Quantification, name: quantification, tools: [kallisto, salmon], default: kallisto },\n        { title: Differential expression, name: DE, tools: [edger, deseq2], default: edger },\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        name: \"group_file\",\n        type: \"input_file\",\n        value: \"\",\n        label: \"Group file (TSV with col1(sample name), col2 (group)): \",\n      },\n    ],\n}\n"
    }
]