[
    {
        "id": "interop",
        "name": "interop",
        "article": "",
        "website": "https:\/\/illumina.github.io\/interop\/index.html",
        "git": "https:\/\/github.com\/Illumina\/interop",
        "description": "The Illumina InterOp libraries are a set of common routines used for reading and writing InterOp metric files.",
        "version": "1.2.4",
        "documentation": "https:\/\/illumina.github.io\/interop\/pages.html",
        "multiqc": "interop",
        "commands": [
            {
                "name": "interop",
                "cname": "Interop",
                "command": "",
                "category": "visualization",
                "output_dir": "interop",
                "inputs": [
                    {
                        "name": "illumina_dir",
                        "type": "illumina_dir",
                        "description": "InterOp metric directory"
                    }
                ],
                "outputs": [
                    {
                        "name": "summary",
                        "type": "csv",
                        "file": "summary.csv",
                        "description": "Summary table"
                    },
                    {
                        "name": "index_summary",
                        "type": "csv",
                        "file": "index_summary_mqc.csv",
                        "description": "Index summary table"
                    },
                    {
                        "name": "dump_text",
                        "type": "csv",
                        "file": "dump_text.csv",
                        "description": "All Interop data as tables"
                    }
                ],
                "options": [
                    {
                        "name": "interop_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "interop": [
                "Robert Langlois, Illumina InterOp libraries, (2016), GitHub repository, https:\/\/github.com\/Illumina\/interop"
            ]
        },
        "yaml": "{\n  id: interop,\n  name: interop,\n  article: '',\n  website: 'https:\/\/illumina.github.io\/interop\/index.html',\n  git: 'https:\/\/github.com\/Illumina\/interop',\n  description: 'The Illumina InterOp libraries are a set of common routines used for reading and writing InterOp metric files.',\n  version: '1.2.4',\n  documentation: 'https:\/\/illumina.github.io\/interop\/pages.html',\n  multiqc: \"interop\",\n  commands:\n    [\n      {\n        name: interop,\n        cname: \"Interop\",\n        command: '',\n        category: \"visualization\",\n        output_dir: interop,\n        inputs: [{ name: \"illumina_dir\", type: \"illumina_dir\", description: \"InterOp metric directory\" }],\n        outputs:\n          [\n            { name: summary, type: \"csv\", file: summary.csv, description: \"Summary table\" },\n            { name: index_summary, type: \"csv\", file: index_summary_mqc.csv, description: \"Index summary table\" },\n            { name: dump_text, type: \"csv\", file: dump_text.csv, description: \"All Interop data as tables\" },\n          ],\n        options:\n           [\n        #     {\n        #       name: \"interop_analysis_dir\",\n        #       type: \"input_dir\",\n        #       value: \"\/Data\",\n        #       label: \"Data directory: \",\n        #       volumes:  [Data: \"\/Data\", Results: \"\/Results\"]\n        #     },\n              {\n                name: \"interop_threads\",\n                prefix: \"--threads\",\n                value: 16,\n                min: 1,\n                max: 64,\n                step: 1,\n                label: \"Threads to use\",\n                type: \"numeric\",\n              },\n           ],\n      },\n    ],\n  install: {\n    # gawk: [ apt-get install gawk ],\n    # interop:\n    # [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/Illumina\/interop\/releases\/download\/v1.1.8\/InterOp-1.1.8-Linux-GNU.tar.gz\",\n    #   \"tar -xvzf InterOp-1.1.8-Linux-GNU.tar.gz\",\n    #   \"rm InterOp-1.1.8-Linux-GNU.tar.gz\",\n    #   \"ENV PATH \/opt\/biotools\/InterOp-1.1.8-Linux-GNU\/bin\/:$PATH\",\n    # ],\n    # gnuplot: [\n    #   \"apt -y update && apt install -y gnuplot\"\n    # ]\n  },\n  citations:  {\n    interop: [\n      \"Robert Langlois, Illumina InterOp libraries, (2016), GitHub repository, https:\/\/github.com\/Illumina\/interop\"\n    ],\n  }\n}"
    }
]