[
    {
        "id": "fastqc",
        "name": "FastQC",
        "article": null,
        "website": "https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/",
        "git": "https:\/\/github.com\/s-andrews\/FastQC",
        "description": "A quality control tool for high throughput raw sequence data.",
        "version": "0.12.1",
        "documentation": "http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/Help\/",
        "multiqc": "fastqc",
        "commands": [
            {
                "name": "fastqc_SE",
                "cname": "Fastqc SE",
                "command": "fastqc",
                "category": "quality",
                "output_dir": "fastqc_SE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "logFile",
                        "type": "txt",
                        "file": "{sample}_fastqc_log.txt",
                        "description": "log fastqc"
                    }
                ],
                "options": []
            },
            {
                "name": "fastqc_PE",
                "cname": "Fastqc PE",
                "command": "fastqc",
                "category": "quality",
                "output_dir": "fastqc_PE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "read2",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "logFile",
                        "type": "txt",
                        "file": "{sample}_fastqc_log.txt",
                        "description": "log fastqc"
                    }
                ],
                "options": []
            }
        ],
        "install": [],
        "citations": {
            "fastqc": [
                "Andrews, S. (2010). FASTQC. A quality control tool for high throughput sequence data"
            ]
        },
        "yaml": "{\n  id: fastqc,\n  name: FastQC,\n  article: ~,\n  website: \"https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/\",\n  git: \"https:\/\/github.com\/s-andrews\/FastQC\",\n  description: \"A quality control tool for high throughput raw sequence data.\",\n  version: \"0.12.1\",\n  documentation: \"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/Help\/\",\n  multiqc: \"fastqc\",\n  commands:\n    [\n      {\n        name: fastqc_SE,\n        cname: \"Fastqc SE\",\n        command: fastqc,\n        category: \"quality\",\n        output_dir: fastqc_SE,\n        inputs: [{ name: read, type: \"reads\" }],\n        outputs:\n          [\n            #{ name: html, type: \"html\", file: \"{sample}_fastqc.html\", description: \"Rapport html fastqc\" },\n            #{ name: zip, type: \"zip\", file: \"{sample}_fastqc.zip\", description: \"Dossier zip fastqc\" },\n            { name: logFile, type: \"txt\", file: \"{sample}_fastqc_log.txt\", description: \"log fastqc\" },\n          ],\n        options:\n          [\n          ],\n      },\n      {\n        name: fastqc_PE,\n        cname: \"Fastqc PE\",\n        command: fastqc,\n        category: \"quality\",\n        output_dir: fastqc_PE,\n        inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }],\n        outputs:\n          [\n            #{ name: html1, type: \"html\", file: \"{sample}_<R>1_fastqc.html\", description: \"Rapport html fastqc\" },\n            #{ name: zip1, type: \"zip\", file: \"{sample}_<R>1_fastqc.zip\", description: \"Dossier zip fastqc\" },\n            #{ name: html2, type: \"html\", file: \"{sample}_<R>2_fastqc.html\", description: \"Rapport html fastqc\" },\n            #{ name: zip2, type: \"zip\", file: \"{sample}_<R>2_fastqc.zip\", description: \"Dossier zip fastqc\" },\n            { name: logFile, type: \"txt\", file: \"{sample}_fastqc_log.txt\", description: \"log fastqc\" },\n          ],\n        options:\n          [\n          ],\n      },\n    ],\n  install: {\n    # fastqc: [\"apt -y update && apt install -y fastqc=0.11.9+dfsg-4\",\n    #          \"sed -i 's\/memory = 250\/memory = 500\/' \/usr\/bin\/fastqc\"]\n  },\n  citations:  {\n    fastqc: [\n      \"Andrews, S. (2010). FASTQC. A quality control tool for high throughput sequence data\"\n    ]\n  }\n}\n"
    }
]