[
    {
        "id": "guppy",
        "name": "guppy",
        "article": "https:\/\/nanoporetech.com\/",
        "website": "https:\/\/community.nanoporetech.com\/protocols\/Guppy-protocol",
        "git": "https:\/\/community.nanoporetech.com\/downloads",
        "description": "Basecalling, the process of converting raw signal data into a sequence",
        "version": "latest",
        "documentation": "https:\/\/nanoporetech.com\/nanopore-sequencing-data-analysis",
        "multiqc": "custom",
        "commands": [
            {
                "name": "guppy",
                "command": "\/opt\/biotools\/ont-guppy\/bin\/guppy_basecaller",
                "category": "basecalling",
                "output_dir": "guppy",
                "inputs": [
                    {
                        "name": "fast5_dir",
                        "type": "fast5_dir",
                        "description": "Directory containing the ONT raw data"
                    }
                ],
                "outputs": [
                    {
                        "name": "sequencing_summary",
                        "type": "tsv",
                        "file": "sequencing_summary.txt",
                        "description": "Table containing sequencing summary"
                    },
                    {
                        "name": "readPass",
                        "type": "reads",
                        "file": "guppy_pass.fq.gz",
                        "description": "File containing reads with an average quality score > Q7"
                    },
                    {
                        "name": "readFail",
                        "type": "reads",
                        "file": "guppy_fail.fq.gz",
                        "description": "File containing reads with an average quality score < Q7"
                    }
                ],
                "options": [
                    {
                        "name": "guppy_gpu_num_callers",
                        "prefix": "--num_callers",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Number of parallel basecallers to create.",
                        "type": "numeric"
                    },
                    {
                        "name": "guppy_gpu_runners_per_device",
                        "prefix": "--gpu_runners_per_device",
                        "value": 1,
                        "min": 1,
                        "max": 4,
                        "step": 1,
                        "label": "Number of runners per GPU device",
                        "type": "numeric"
                    },
                    {
                        "name": "guppy_config_file",
                        "prefix": "",
                        "type": "select",
                        "choices": [
                            {
                                "dna_r10.3_450bps_hac.cfg": "dna_r10.3_450bps_hac.cfg"
                            },
                            {
                                "dna_r10.3_450bps_hac_prom.cfg": "dna_r10.3_450bps_hac_prom.cfg"
                            },
                            {
                                "dna_r10.3_450bps_modbases_5mc_hac_prom.cfg": "dna_r10.3_450bps_modbases_5mc_hac_prom.cfg"
                            },
                            {
                                "dna_r10.3_450bps_sup.cfg": "dna_r10.3_450bps_sup.cfg"
                            },
                            {
                                "dna_r10_450bps_hac.cfg": "dna_r10_450bps_hac.cfg"
                            },
                            {
                                "dna_r10.4_e8.1_hac.cfg": "dna_r10.4_e8.1_hac.cfg"
                            },
                            {
                                "dna_r10.4_e8.1_hac_prom.cfg": "dna_r10.4_e8.1_hac_prom.cfg"
                            },
                            {
                                "dna_r10.4_e8.1_sup.cfg": "dna_r10.4_e8.1_sup.cfg"
                            },
                            {
                                "dna_r9.4.1_450bps_hac.cfg": "dna_r9.4.1_450bps_hac.cfg"
                            },
                            {
                                "dna_r9.4.1_450bps_hac_prom.cfg": "dna_r9.4.1_450bps_hac_prom.cfg"
                            },
                            {
                                "dna_r9.4.1_450bps_hac_prom_fw205.cfg": "dna_r9.4.1_450bps_hac_prom_fw205.cfg"
                            },
                            {
                                "dna_r9.4.1_450bps_modbases_5mc_hac.cfg": "dna_r9.4.1_450bps_modbases_5mc_hac.cfg"
                            },
                            {
                                "dna_r9.4.1_450bps_modbases_5mc_hac_prom.cfg": "dna_r9.4.1_450bps_modbases_5mc_hac_prom.cfg"
                            },
                            {
                                "dna_r9.4.1_450bps_sup.cfg": "dna_r9.4.1_450bps_sup.cfg"
                            },
                            {
                                "dna_r9.4.1_450bps_sup_prom.cfg": "dna_r9.4.1_450bps_sup_prom.cfg"
                            },
                            {
                                "rna_r9.4.1_70bps_hac.cfg": "rna_r9.4.1_70bps_hac.cfg"
                            },
                            {
                                "rna_r9.4.1_70bps_hac_prom.cfg": "rna_r9.4.1_70bps_hac_prom.cfg"
                            }
                        ],
                        "value": "dna_r9.4.1_450bps_hac.cfg",
                        "label": "Config file"
                    }
                ]
            }
        ],
        "install": {
            "guppy": [
                "cd \/opt\/biotools",
                "tar -zxvf ont-guppy_5.0.16_linux64.tar.gz",
                "ENV PATH $PATH:\/opt\/biotools\/ont-guppy\/bin"
            ],
            "cuda": [
                "apt-get install -y cuda-10-1 ",
                "apt-get install -y libcudnn7"
            ]
        },
        "citations": {
            "guppy": [
                "guppy basecaller from https:\/\/nanoporetech.com\/"
            ]
        },
        "yaml": "{\n  id: guppy,\n  name: guppy,\n  article:  \"https:\/\/nanoporetech.com\/\",\n  website: \"https:\/\/community.nanoporetech.com\/protocols\/Guppy-protocol\",\n  git: \"https:\/\/community.nanoporetech.com\/downloads\",\n  description: \"Basecalling, the process of converting raw signal data into a sequence\",\n  version: \"latest\",\n  documentation: \"https:\/\/nanoporetech.com\/nanopore-sequencing-data-analysis\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: guppy,\n        command: \/opt\/biotools\/ont-guppy\/bin\/guppy_basecaller ,\n        category: \"basecalling\",\n        output_dir: guppy,\n        inputs: [\n          { name: \"fast5_dir\", type: \"fast5_dir\", description: \"Directory containing the ONT raw data\" },\n        ],\n        outputs:\n          [\n            { name: sequencing_summary, type: \"tsv\", file: \"sequencing_summary.txt\", description: \"Table containing sequencing summary\" },\n            { name: readPass, type: \"reads\", file: \"guppy_pass.fq.gz\", description: \"File containing reads with an average quality score > Q7\" },\n            { name: readFail, type: \"reads\", file: \"guppy_fail.fq.gz\", description: \"File containing reads with an average quality score < Q7\" },\n          ],\n        options:\n          [\n            {\n              name: \"guppy_gpu_num_callers\",\n              prefix: \"--num_callers\",\n              value: 16,\n              min: 1,\n              max: 64,\n              step: 1,\n              label: \"Number of parallel basecallers to create.\",\n              type: \"numeric\",\n            },\n            { \n              name: \"guppy_gpu_runners_per_device\",\n              prefix: \"--gpu_runners_per_device\",\n              value: 1,\n              min: 1,\n              max: 4,\n              step: 1,\n              label: \"Number of runners per GPU device\",\n              type: \"numeric\",\n            },\n            {\n              name: \"guppy_config_file\",\n              prefix: \"\",\n              type: \"select\",\n              choices:\n              [\n                dna_r10.3_450bps_hac.cfg : \"dna_r10.3_450bps_hac.cfg\",\n                dna_r10.3_450bps_hac_prom.cfg : \"dna_r10.3_450bps_hac_prom.cfg\",\n                dna_r10.3_450bps_modbases_5mc_hac_prom.cfg : \"dna_r10.3_450bps_modbases_5mc_hac_prom.cfg\",\n                dna_r10.3_450bps_sup.cfg : \"dna_r10.3_450bps_sup.cfg\",\n                dna_r10_450bps_hac.cfg : \"dna_r10_450bps_hac.cfg\",\n                dna_r10.4_e8.1_hac.cfg : \"dna_r10.4_e8.1_hac.cfg\",\n                dna_r10.4_e8.1_hac_prom.cfg : \"dna_r10.4_e8.1_hac_prom.cfg\",\n                dna_r10.4_e8.1_sup.cfg : \"dna_r10.4_e8.1_sup.cfg\",\n                dna_r9.4.1_450bps_hac.cfg : \"dna_r9.4.1_450bps_hac.cfg\",\n                dna_r9.4.1_450bps_hac_prom.cfg : \"dna_r9.4.1_450bps_hac_prom.cfg\",\n                dna_r9.4.1_450bps_hac_prom_fw205.cfg : \"dna_r9.4.1_450bps_hac_prom_fw205.cfg\",\n                dna_r9.4.1_450bps_modbases_5mc_hac.cfg : \"dna_r9.4.1_450bps_modbases_5mc_hac.cfg\",\n                dna_r9.4.1_450bps_modbases_5mc_hac_prom.cfg : \"dna_r9.4.1_450bps_modbases_5mc_hac_prom.cfg\",\n                dna_r9.4.1_450bps_sup.cfg : \"dna_r9.4.1_450bps_sup.cfg\",\n                dna_r9.4.1_450bps_sup_prom.cfg : \"dna_r9.4.1_450bps_sup_prom.cfg\",\n                rna_r9.4.1_70bps_hac.cfg : \"rna_r9.4.1_70bps_hac.cfg\",\n                rna_r9.4.1_70bps_hac_prom.cfg : \"rna_r9.4.1_70bps_hac_prom.cfg\",\n              ],\n              value: \"dna_r9.4.1_450bps_hac.cfg\",\n              label: \"Config file\",\n            }\n          ],\n      },\n    ],\n  install:\n    {\n      guppy: [\n        \"cd \/opt\/biotools\",\n        \"tar -zxvf ont-guppy_5.0.16_linux64.tar.gz\",\n        \"ENV PATH $PATH:\/opt\/biotools\/ont-guppy\/bin\"\n      ],\n      cuda: [\n        'apt-get install -y cuda-10-1 ',\n        'apt-get install -y libcudnn7'\n      ],\n    },\n    citations:  {\n      guppy: [\n        \"guppy basecaller from https:\/\/nanoporetech.com\/\"\n      ]\n    }\n}\n"
    }
]